diff --git a/pkg/iac/scanners/terraform/parser/evaluator.go b/pkg/iac/scanners/terraform/parser/evaluator.go
index a203451245ff..40391e6a1249 100644
--- a/pkg/iac/scanners/terraform/parser/evaluator.go
+++ b/pkg/iac/scanners/terraform/parser/evaluator.go
@@ -191,18 +191,10 @@ func (e *evaluator) EvaluateAll(ctx context.Context) (terraform.Modules, map[str
 
 	e.debug.Log("Module evaluation complete.")
 	parseDuration += time.Since(start)
-	rootModule := terraform.NewModule(e.projectRootPath, e.modulePath, e.blocks, e.ignores, e.isModuleLocal())
-	for _, m := range modules {
-		m.SetParent(rootModule)
-	}
+	rootModule := terraform.NewModule(e.projectRootPath, e.modulePath, e.blocks, e.ignores)
 	return append(terraform.Modules{rootModule}, modules...), fsMap, parseDuration
 }
 
-func (e *evaluator) isModuleLocal() bool {
-	// the module source is empty only for local modules
-	return e.parentParser.moduleSource == ""
-}
-
 func (e *evaluator) expandBlocks(blocks terraform.Blocks) terraform.Blocks {
 	return e.expandDynamicBlocks(e.expandBlockForEaches(e.expandBlockCounts(blocks), false)...)
 }
diff --git a/pkg/iac/scanners/terraform/parser/modules.go b/pkg/iac/scanners/terraform/parser/modules.go
new file mode 100644
index 000000000000..499fc2fb9647
--- /dev/null
+++ b/pkg/iac/scanners/terraform/parser/modules.go
@@ -0,0 +1,78 @@
+package parser
+
+import (
+	"context"
+	"path"
+	"sort"
+	"strings"
+
+	"github.com/samber/lo"
+	"github.com/zclconf/go-cty/cty"
+
+	"github.com/aquasecurity/trivy/pkg/iac/terraform"
+)
+
+// FindRootModules takes a list of module paths and identifies the root local modules.
+// It builds a graph based on the module dependencies and determines the modules that have no incoming dependencies,
+// considering them as root modules.
+func (p *Parser) FindRootModules(ctx context.Context, dirs []string) ([]string, error) {
+	for _, dir := range dirs {
+		if err := p.ParseFS(ctx, dir); err != nil {
+			return nil, err
+		}
+	}
+
+	blocks, _, err := p.readBlocks(p.files)
+	if err != nil {
+		return nil, err
+	}
+
+	g := buildGraph(blocks, dirs)
+	rootModules := g.rootModules()
+	sort.Strings(rootModules)
+	return rootModules, nil
+}
+
+type modulesGraph map[string][]string
+
+func buildGraph(blocks terraform.Blocks, paths []string) modulesGraph {
+	moduleBlocks := blocks.OfType("module")
+
+	graph := lo.SliceToMap(paths, func(p string) (string, []string) {
+		return p, nil
+	})
+
+	for _, block := range moduleBlocks {
+		sourceVal := block.GetAttribute("source").Value()
+		if sourceVal.Type() != cty.String {
+			continue
+		}
+
+		source := sourceVal.AsString()
+		if strings.HasPrefix(source, ".") {
+			filename := block.GetMetadata().Range().GetFilename()
+			dir := path.Dir(filename)
+			graph[dir] = append(graph[dir], path.Join(dir, source))
+		}
+	}
+
+	return graph
+}
+
+func (g modulesGraph) rootModules() []string {
+	incomingEdges := make(map[string]int)
+	for _, neighbors := range g {
+		for _, neighbor := range neighbors {
+			incomingEdges[neighbor]++
+		}
+	}
+
+	var roots []string
+	for module := range g {
+		if incomingEdges[module] == 0 {
+			roots = append(roots, module)
+		}
+	}
+
+	return roots
+}
diff --git a/pkg/iac/scanners/terraform/parser/modules_test.go b/pkg/iac/scanners/terraform/parser/modules_test.go
new file mode 100644
index 000000000000..142783160f01
--- /dev/null
+++ b/pkg/iac/scanners/terraform/parser/modules_test.go
@@ -0,0 +1,71 @@
+package parser
+
+import (
+	"context"
+	"path"
+	"testing"
+
+	"github.com/aquasecurity/trivy/internal/testutil"
+	"github.com/samber/lo"
+	"github.com/stretchr/testify/assert"
+	"github.com/stretchr/testify/require"
+	"golang.org/x/exp/maps"
+)
+
+func TestFindRootModules(t *testing.T) {
+	tests := []struct {
+		name     string
+		files    map[string]string
+		expected []string
+	}{
+		{
+			name: "multiple root modules",
+			files: map[string]string{
+				"code/main.tf": `
+module "this" {
+  count = 0
+  source = "./modules/s3"
+}`,
+				"code/modules/s3/main.tf": `
+module "this" {
+  source = "./modules/logging"
+}
+resource "aws_s3_bucket" "this" {
+  bucket = "test"
+}`,
+				"code/modules/s3/modules/logging/main.tf": `
+resource "aws_s3_bucket" "this" {
+  bucket = "test1"
+}`,
+				"code/example/main.tf": `
+module "this" {
+  source = "../modules/s3"
+}`,
+			},
+			expected: []string{"code", "code/example"},
+		},
+		{
+			name: "without module block",
+			files: map[string]string{
+				"code/infra1/main.tf": `resource "test" "this" {}`,
+				"code/infra2/main.tf": `resource "test" "this" {}`,
+			},
+			expected: []string{"code/infra1", "code/infra2"},
+		},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			fsys := testutil.CreateFS(t, tt.files)
+			parser := New(fsys, "", OptionStopOnHCLError(true))
+
+			modules := lo.Map(maps.Keys(tt.files), func(p string, _ int) string {
+				return path.Dir(p)
+			})
+
+			got, err := parser.FindRootModules(context.TODO(), modules)
+			require.NoError(t, err)
+			assert.Equal(t, tt.expected, got)
+		})
+	}
+}
diff --git a/pkg/iac/scanners/terraform/parser/parser_test.go b/pkg/iac/scanners/terraform/parser/parser_test.go
index c8c6d727c112..12594841251b 100644
--- a/pkg/iac/scanners/terraform/parser/parser_test.go
+++ b/pkg/iac/scanners/terraform/parser/parser_test.go
@@ -1271,6 +1271,96 @@ func TestForEachWithObjectsOfDifferentTypes(t *testing.T) {
 	assert.Len(t, modules, 1)
 }
 
+func TestCountMetaArgument(t *testing.T) {
+	tests := []struct {
+		name     string
+		src      string
+		expected int
+	}{
+		{
+			name: "zero resources",
+			src: `resource "test" "this" {
+  count = 0
+}`,
+			expected: 0,
+		},
+		{
+			name: "several resources",
+			src: `resource "test" "this" {
+  count = 2
+}`,
+			expected: 2,
+		},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			fsys := testutil.CreateFS(t, map[string]string{
+				"main.tf": tt.src,
+			})
+			parser := New(fsys, "", OptionStopOnHCLError(true))
+			require.NoError(t, parser.ParseFS(context.TODO(), "."))
+
+			modules, _, err := parser.EvaluateAll(context.TODO())
+			require.NoError(t, err)
+			assert.Len(t, modules, 1)
+
+			resources := modules.GetResourcesByType("test")
+			assert.Len(t, resources, tt.expected)
+		})
+	}
+}
+
+func TestCountMetaArgumentInModule(t *testing.T) {
+	tests := []struct {
+		name                   string
+		files                  map[string]string
+		expectedCountModules   int
+		expectedCountResources int
+	}{
+		{
+			name: "zero modules",
+			files: map[string]string{
+				"main.tf": `module "this" {
+  count = 0
+  source = "./modules/test"
+}`,
+				"modules/test/main.tf": `resource "test" "this" {}`,
+			},
+			expectedCountModules:   1,
+			expectedCountResources: 0,
+		},
+		{
+			name: "several modules",
+			files: map[string]string{
+				"main.tf": `module "this" {
+  count = 2
+  source = "./modules/test"
+}`,
+				"modules/test/main.tf": `resource "test" "this" {}`,
+			},
+			expectedCountModules:   3,
+			expectedCountResources: 2,
+		},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			fsys := testutil.CreateFS(t, tt.files)
+			parser := New(fsys, "", OptionStopOnHCLError(true))
+			require.NoError(t, parser.ParseFS(context.TODO(), "."))
+
+			modules, _, err := parser.EvaluateAll(context.TODO())
+			require.NoError(t, err)
+
+			assert.Len(t, modules, tt.expectedCountModules)
+
+			resources := modules.GetResourcesByType("test")
+			assert.Len(t, resources, tt.expectedCountResources)
+		})
+	}
+}
+
 func TestDynamicBlocks(t *testing.T) {
 	t.Run("arg is list of int", func(t *testing.T) {
 		modules := parse(t, map[string]string{
diff --git a/pkg/iac/scanners/terraform/scanner.go b/pkg/iac/scanners/terraform/scanner.go
index a3d48bf8f629..5176b6471355 100644
--- a/pkg/iac/scanners/terraform/scanner.go
+++ b/pkg/iac/scanners/terraform/scanner.go
@@ -2,6 +2,7 @@ package terraform
 
 import (
 	"context"
+	"fmt"
 	"io"
 	"io/fs"
 	"path"
@@ -11,8 +12,6 @@ import (
 	"sync"
 	"time"
 
-	"golang.org/x/exp/slices"
-
 	"github.com/aquasecurity/trivy/pkg/extrafs"
 	"github.com/aquasecurity/trivy/pkg/iac/debug"
 	"github.com/aquasecurity/trivy/pkg/iac/framework"
@@ -20,7 +19,7 @@ import (
 	"github.com/aquasecurity/trivy/pkg/iac/scan"
 	"github.com/aquasecurity/trivy/pkg/iac/scanners"
 	"github.com/aquasecurity/trivy/pkg/iac/scanners/options"
-	executor2 "github.com/aquasecurity/trivy/pkg/iac/scanners/terraform/executor"
+	"github.com/aquasecurity/trivy/pkg/iac/scanners/terraform/executor"
 	"github.com/aquasecurity/trivy/pkg/iac/scanners/terraform/parser"
 	"github.com/aquasecurity/trivy/pkg/iac/scanners/terraform/parser/resolvers"
 	"github.com/aquasecurity/trivy/pkg/iac/terraform"
@@ -35,7 +34,7 @@ type Scanner struct { // nolint: gocritic
 	sync.Mutex
 	options               []options.ScannerOption
 	parserOpt             []options.ParserOption
-	executorOpt           []executor2.Option
+	executorOpt           []executor.Option
 	dirs                  map[string]struct{}
 	forceAllDirs          bool
 	policyDirs            []string
@@ -54,7 +53,7 @@ func (s *Scanner) SetSpec(spec string) {
 }
 
 func (s *Scanner) SetRegoOnly(regoOnly bool) {
-	s.executorOpt = append(s.executorOpt, executor2.OptionWithRegoOnly(regoOnly))
+	s.executorOpt = append(s.executorOpt, executor.OptionWithRegoOnly(regoOnly))
 }
 
 func (s *Scanner) SetFrameworks(frameworks []framework.Framework) {
@@ -81,7 +80,7 @@ func (s *Scanner) AddParserOptions(opts ...options.ParserOption) {
 	s.parserOpt = append(s.parserOpt, opts...)
 }
 
-func (s *Scanner) AddExecutorOptions(opts ...executor2.Option) {
+func (s *Scanner) AddExecutorOptions(opts ...executor.Option) {
 	s.executorOpt = append(s.executorOpt, opts...)
 }
 
@@ -95,7 +94,7 @@ func (s *Scanner) SetSkipRequiredCheck(skip bool) {
 
 func (s *Scanner) SetDebugWriter(writer io.Writer) {
 	s.parserOpt = append(s.parserOpt, options.ParserWithDebug(writer))
-	s.executorOpt = append(s.executorOpt, executor2.OptionWithDebugWriter(writer))
+	s.executorOpt = append(s.executorOpt, executor.OptionWithDebugWriter(writer))
 	s.debug = debug.New(writer, "terraform", "scanner")
 }
 
@@ -123,7 +122,7 @@ func (s *Scanner) SetRegoErrorLimit(_ int) {}
 
 type Metrics struct {
 	Parser   parser.Metrics
-	Executor executor2.Metrics
+	Executor executor.Metrics
 	Timings  struct {
 		Total time.Duration
 	}
@@ -168,36 +167,17 @@ type terraformRootModule struct {
 	fsMap    map[string]fs.FS
 }
 
-func excludeNonRootModules(modules []terraformRootModule) []terraformRootModule {
-	var result []terraformRootModule
-	var childPaths []string
-
-	for _, module := range modules {
-		childPaths = append(childPaths, module.childs.ChildModulesPaths()...)
-	}
-
-	for _, module := range modules {
-		// if the path of the root module matches the path of the child module,
-		// then we should not scan it
-		if !slices.Contains(childPaths, module.rootPath) {
-			result = append(result, module)
-		}
-	}
-	return result
-}
-
 func (s *Scanner) ScanFSWithMetrics(ctx context.Context, target fs.FS, dir string) (scan.Results, Metrics, error) {
-
 	var metrics Metrics
 
 	s.debug.Log("Scanning [%s] at '%s'...", target, dir)
 
-	// find directories which directly contain tf files (and have no parent containing tf files)
-	rootDirs := s.findRootModules(target, dir, dir)
-	sort.Strings(rootDirs)
+	// find directories which directly contain tf files
+	modulePaths := s.findModules(target, dir, dir)
+	sort.Strings(modulePaths)
 
-	if len(rootDirs) == 0 {
-		s.debug.Log("no root modules found")
+	if len(modulePaths) == 0 {
+		s.debug.Log("no modules found")
 		return nil, metrics, nil
 	}
 
@@ -207,13 +187,20 @@ func (s *Scanner) ScanFSWithMetrics(ctx context.Context, target fs.FS, dir strin
 	}
 
 	s.execLock.Lock()
-	s.executorOpt = append(s.executorOpt, executor2.OptionWithRegoScanner(regoScanner), executor2.OptionWithFrameworks(s.frameworks...))
+	s.executorOpt = append(s.executorOpt, executor.OptionWithRegoScanner(regoScanner), executor.OptionWithFrameworks(s.frameworks...))
 	s.execLock.Unlock()
 
 	var allResults scan.Results
 
+	p := parser.New(target, "", s.parserOpt...)
+	rootDirs, err := p.FindRootModules(ctx, modulePaths)
+	if err != nil {
+		return nil, metrics, fmt.Errorf("failed to find root modules: %w", err)
+	}
+
+	rootModules := make([]terraformRootModule, 0, len(rootDirs))
+
 	// parse all root module directories
-	var rootModules []terraformRootModule
 	for _, dir := range rootDirs {
 
 		s.debug.Log("Scanning root module '%s'...", dir)
@@ -243,10 +230,9 @@ func (s *Scanner) ScanFSWithMetrics(ctx context.Context, target fs.FS, dir strin
 		})
 	}
 
-	rootModules = excludeNonRootModules(rootModules)
 	for _, module := range rootModules {
 		s.execLock.RLock()
-		e := executor2.New(s.executorOpt...)
+		e := executor.New(s.executorOpt...)
 		s.execLock.RUnlock()
 		results, execMetrics, err := e.Execute(module.childs)
 		if err != nil {
@@ -316,7 +302,7 @@ func (s *Scanner) removeNestedDirs(dirs []string) []string {
 	return clean
 }
 
-func (s *Scanner) findRootModules(target fs.FS, scanDir string, dirs ...string) []string {
+func (s *Scanner) findModules(target fs.FS, scanDir string, dirs ...string) []string {
 
 	var roots []string
 	var others []string
@@ -358,7 +344,7 @@ func (s *Scanner) findRootModules(target fs.FS, scanDir string, dirs ...string)
 	}
 
 	if (len(roots) == 0 || s.forceAllDirs) && len(others) > 0 {
-		roots = append(roots, s.findRootModules(target, scanDir, others...)...)
+		roots = append(roots, s.findModules(target, scanDir, others...)...)
 	}
 
 	return s.removeNestedDirs(roots)
diff --git a/pkg/iac/scanners/terraform/scanner_test.go b/pkg/iac/scanners/terraform/scanner_test.go
index 130427d9f5b4..9e44893e0ff7 100644
--- a/pkg/iac/scanners/terraform/scanner_test.go
+++ b/pkg/iac/scanners/terraform/scanner_test.go
@@ -1321,3 +1321,72 @@ deny[res] {
 		fmt.Printf("Debug logs:\n%s\n", debugLog.String())
 	}
 }
+
+func TestScanModuleWithCount(t *testing.T) {
+	fs := testutil.CreateFS(t, map[string]string{
+		"code/main.tf": `
+module "this" {
+  count = 0
+  source = "./modules/s3"
+}`,
+		"code/modules/s3/main.tf": `
+module "this" {
+  source = "./modules/logging"
+}
+resource "aws_s3_bucket" "this" {
+  bucket = "test"
+}`,
+		"code/modules/s3/modules/logging/main.tf": `
+resource "aws_s3_bucket" "this" {
+  bucket = "test1"
+}`,
+		"code/example/main.tf": `
+module "this" {
+  source = "../modules/s3"
+}`,
+		"rules/region.rego": `
+# METADATA
+# schemas:
+# - input: schema.input
+# custom:
+#   avd_id: AVD-AWS-0001
+#   input:
+#     selector:
+#     - type: cloud
+#       subtypes:
+#         - service: s3
+#           provider: aws
+package user.test.aws1
+deny[res] {
+	bucket := input.aws.s3.buckets[_]
+	bucket.name.value == "test"
+  res := result.new("bucket with test name is not allowed!", bucket)
+}
+`,
+	})
+
+	debugLog := bytes.NewBuffer([]byte{})
+	scanner := New(
+		options.ScannerWithDebug(debugLog),
+		options.ScannerWithPolicyDirs("rules"),
+		options.ScannerWithPolicyFilesystem(fs),
+		options.ScannerWithRegoOnly(true),
+		options.ScannerWithPolicyNamespaces("user"),
+		options.ScannerWithEmbeddedLibraries(false),
+		options.ScannerWithEmbeddedPolicies(false),
+		options.ScannerWithRegoErrorLimits(0),
+		ScannerWithAllDirectories(true),
+	)
+
+	results, err := scanner.ScanFS(context.TODO(), fs, "code")
+	require.NoError(t, err)
+
+	require.Len(t, results, 1)
+
+	failed := results.GetFailed()
+
+	assert.Len(t, failed, 1)
+
+	occurrences := failed[0].Occurrences()
+	assert.Equal(t, "code/example/main.tf", occurrences[0].Filename)
+}
diff --git a/pkg/iac/terraform/module.go b/pkg/iac/terraform/module.go
index 73cb01d2048c..dd89fa2bd40d 100644
--- a/pkg/iac/terraform/module.go
+++ b/pkg/iac/terraform/module.go
@@ -12,10 +12,9 @@ type Module struct {
 	modulePath string
 	ignores    Ignores
 	parent     *Module
-	local      bool
 }
 
-func NewModule(rootPath, modulePath string, blocks Blocks, ignores Ignores, local bool) *Module {
+func NewModule(rootPath, modulePath string, blocks Blocks, ignores Ignores) *Module {
 
 	blockMap := make(map[string]Blocks)
 
@@ -31,7 +30,6 @@ func NewModule(rootPath, modulePath string, blocks Blocks, ignores Ignores, loca
 		blockMap:   blockMap,
 		rootPath:   rootPath,
 		modulePath: modulePath,
-		local:      local,
 	}
 }
 
diff --git a/pkg/iac/terraform/modules.go b/pkg/iac/terraform/modules.go
index 9272f2096145..8a9cad25c433 100644
--- a/pkg/iac/terraform/modules.go
+++ b/pkg/iac/terraform/modules.go
@@ -8,16 +8,6 @@ import (
 
 type Modules []*Module
 
-func (m Modules) ChildModulesPaths() []string {
-	var result []string
-	for _, module := range m {
-		if module.parent != nil && module.local {
-			result = append(result, module.modulePath)
-		}
-	}
-	return result
-}
-
 type ResourceIDResolutions map[string]bool
 
 func (r ResourceIDResolutions) Resolve(id string) {