diff --git a/src/learner.cc b/src/learner.cc
index 9aceb70a9d3a..47080a5c12b9 100644
--- a/src/learner.cc
+++ b/src/learner.cc
@@ -1119,6 +1119,10 @@ class LearnerImpl : public LearnerIO {
                "booster.";
       }
     }
+
+    if (p_fmat->Info().num_row_ == 0) {
+      LOG(WARNING) << "Empty dataset at worker: " << rabit::GetRank();
+    }
   }
 
  private:
diff --git a/src/metric/elementwise_metric.cu b/src/metric/elementwise_metric.cu
index 85dead9c3d98..f57ac54e68e3 100644
--- a/src/metric/elementwise_metric.cu
+++ b/src/metric/elementwise_metric.cu
@@ -332,9 +332,6 @@ struct EvalEWiseBase : public Metric {
   bst_float Eval(const HostDeviceVector<bst_float>& preds,
                  const MetaInfo& info,
                  bool distributed) override {
-    if (info.labels_.Size() == 0) {
-      LOG(WARNING) << "label set is empty";
-    }
     CHECK_EQ(preds.Size(), info.labels_.Size())
         << "label and prediction size not match, "
         << "hint: use merror or mlogloss for multi-class classification";
diff --git a/src/objective/regression_obj.cu b/src/objective/regression_obj.cu
index 810ee9a6be4a..e71e1f0353ef 100644
--- a/src/objective/regression_obj.cu
+++ b/src/objective/regression_obj.cu
@@ -55,9 +55,6 @@ class RegLossObj : public ObjFunction {
                    const MetaInfo &info,
                    int iter,
                    HostDeviceVector<GradientPair>* out_gpair) override {
-    if (info.labels_.Size() == 0U) {
-      LOG(WARNING) << "Label set is empty.";
-    }
     CHECK_EQ(preds.Size(), info.labels_.Size())
         << " " << "labels are not correctly provided"
         << "preds.size=" << preds.Size() << ", label.size=" << info.labels_.Size() << ", "