diff --git a/Dockerfile.indigo b/Dockerfile.indigo
index 06c40c7c6..1de7513db 100644
--- a/Dockerfile.indigo
+++ b/Dockerfile.indigo
@@ -14,6 +14,8 @@
 
 FROM ros:indigo
 
+ARG CARTOGRAPHER_VERSION=master
+
 # First, we invalidate the entire cache if googlecartographer/cartographer has
 # changed. This file's content changes whenever master changes. See:
 # http://stackoverflow.com/questions/36996046/how-to-prevent-dockerfile-caching-git-clone
@@ -23,10 +25,8 @@ ADD https://api.github.com/repos/googlecartographer/cartographer/git/refs/heads/
 # wstool needs the updated rosinstall file to clone the correct repos.
 COPY cartographer_ros.rosinstall cartographer_ros/
 COPY scripts/prepare_catkin_workspace.sh cartographer_ros/scripts/
-# Remove the contents of the cartographer_ros repo and copy in the updated
-# files as necessary.
-RUN cartographer_ros/scripts/prepare_catkin_workspace.sh && \
-    rm -rf catkin_ws/src/cartographer_ros/*
+RUN CARTOGRAPHER_VERSION=$CARTOGRAPHER_VERSION \
+    cartographer_ros/scripts/prepare_catkin_workspace.sh
 
 # rosdep needs the updated package.xml files to install the correct debs.
 COPY cartographer_ros/package.xml catkin_ws/src/cartographer_ros/cartographer_ros/
diff --git a/Dockerfile.kinetic b/Dockerfile.kinetic
index 51b0f788d..e040ba4f8 100644
--- a/Dockerfile.kinetic
+++ b/Dockerfile.kinetic
@@ -14,6 +14,8 @@
 
 FROM ros:kinetic
 
+ARG CARTOGRAPHER_VERSION=master
+
 # Xenial's base image doesn't ship with sudo.
 RUN apt-get update && apt-get install -y sudo && rm -rf /var/lib/apt/lists/*
 
@@ -26,10 +28,8 @@ ADD https://api.github.com/repos/googlecartographer/cartographer/git/refs/heads/
 # wstool needs the updated rosinstall file to clone the correct repos.
 COPY cartographer_ros.rosinstall cartographer_ros/
 COPY scripts/prepare_catkin_workspace.sh cartographer_ros/scripts/
-# Remove the contents of the cartographer_ros repo and copy in the updated
-# files as necessary.
-RUN cartographer_ros/scripts/prepare_catkin_workspace.sh && \
-    rm -rf catkin_ws/src/cartographer_ros/*
+RUN CARTOGRAPHER_VERSION=$CARTOGRAPHER_VERSION \
+    cartographer_ros/scripts/prepare_catkin_workspace.sh
 
 # rosdep needs the updated package.xml files to install the correct debs.
 COPY cartographer_ros/package.xml catkin_ws/src/cartographer_ros/cartographer_ros/
diff --git a/scripts/prepare_catkin_workspace.sh b/scripts/prepare_catkin_workspace.sh
index b89ed5ae1..7e38d2475 100755
--- a/scripts/prepare_catkin_workspace.sh
+++ b/scripts/prepare_catkin_workspace.sh
@@ -20,10 +20,12 @@ set -o verbose
 . /opt/ros/${ROS_DISTRO}/setup.sh
 
 # Create a new workspace in 'catkin_ws'.
-mkdir catkin_ws
-cd catkin_ws
-wstool init src
+mkdir -p catkin_ws/src
+cd catkin_ws/src
+wstool init
 
 # Merge the cartographer_ros.rosinstall file and fetch code for dependencies.
-wstool merge -t src ../cartographer_ros/cartographer_ros.rosinstall
-wstool update -t src
+wstool merge ../../cartographer_ros/cartographer_ros.rosinstall
+wstool set cartographer -v ${CARTOGRAPHER_VERSION} -y
+wstool remove cartographer_ros
+wstool update