diff --git a/cluster/gce/debian/helper.sh b/cluster/gce/debian/helper.sh
index e24a1b0900c..ad1ac797b1c 100755
--- a/cluster/gce/debian/helper.sh
+++ b/cluster/gce/debian/helper.sh
@@ -39,6 +39,7 @@ function create-master-instance {
   fi
 
   write-master-env
+  prepare-startup-script
   gcloud compute instances create "${MASTER_NAME}" \
     ${address_opt} \
     --project "${PROJECT}" \
@@ -51,7 +52,7 @@ function create-master-instance {
     --scopes "storage-ro,compute-rw,monitoring,logging-write" \
     --can-ip-forward \
     --metadata-from-file \
-      "startup-script=${KUBE_ROOT}/cluster/gce/configure-vm.sh,kube-env=${KUBE_TEMP}/master-kube-env.yaml,cluster-name=${KUBE_TEMP}/cluster-name.txt" \
+      "startup-script=${KUBE_TEMP}/configure-vm.sh,kube-env=${KUBE_TEMP}/master-kube-env.yaml,cluster-name=${KUBE_TEMP}/cluster-name.txt" \
     --disk "name=${MASTER_NAME}-pd,device-name=master-pd,mode=rw,boot=no,auto-delete=no" \
     ${preemptible_master}
 }
@@ -59,8 +60,9 @@ function create-master-instance {
 # $1: template name (required)
 function create-node-instance-template {
   local template_name="$1"
+  prepare-startup-script
   create-node-template "$template_name" "${scope_flags}" \
-    "startup-script=${KUBE_ROOT}/cluster/gce/configure-vm.sh" \
+    "startup-script=${KUBE_TEMP}/configure-vm.sh" \
     "kube-env=${KUBE_TEMP}/node-kube-env.yaml" \
     "cluster-name=${KUBE_TEMP}/cluster-name.txt"
 }
diff --git a/cluster/gce/util.sh b/cluster/gce/util.sh
index bdd22b1c696..ab43491bd7e 100755
--- a/cluster/gce/util.sh
+++ b/cluster/gce/util.sh
@@ -1185,10 +1185,11 @@ function prepare-push() {
 function push-master {
   echo "Updating master metadata ..."
   write-master-env
-  add-instance-metadata-from-file "${KUBE_MASTER}" "kube-env=${KUBE_TEMP}/master-kube-env.yaml" "startup-script=${KUBE_ROOT}/cluster/gce/configure-vm.sh"
+  prepare-startup-script
+  add-instance-metadata-from-file "${KUBE_MASTER}" "kube-env=${KUBE_TEMP}/master-kube-env.yaml" "startup-script=${KUBE_TEMP}/configure-vm.sh"
 
   echo "Pushing to master (log at ${OUTPUT}/push-${KUBE_MASTER}.log) ..."
-  cat ${KUBE_ROOT}/cluster/gce/configure-vm.sh | gcloud compute ssh --ssh-flag="-o LogLevel=quiet" --project "${PROJECT}" --zone "${ZONE}" "${KUBE_MASTER}" --command "sudo bash -s -- --push" &> ${OUTPUT}/push-"${KUBE_MASTER}".log
+  cat ${KUBE_TEMP}/configure-vm.sh | gcloud compute ssh --ssh-flag="-o LogLevel=quiet" --project "${PROJECT}" --zone "${ZONE}" "${KUBE_MASTER}" --command "sudo bash -s -- --push" &> ${OUTPUT}/push-"${KUBE_MASTER}".log
 }
 
 # Push binaries to kubernetes node
@@ -1196,10 +1197,11 @@ function push-node() {
   node=${1}
 
   echo "Updating node ${node} metadata... "
-  add-instance-metadata-from-file "${node}" "kube-env=${KUBE_TEMP}/node-kube-env.yaml" "startup-script=${KUBE_ROOT}/cluster/gce/configure-vm.sh"
+  prepare-startup-script
+  add-instance-metadata-from-file "${node}" "kube-env=${KUBE_TEMP}/node-kube-env.yaml" "startup-script=${KUBE_TEMP}/configure-vm.sh"
 
   echo "Start upgrading node ${node} (log at ${OUTPUT}/push-${node}.log) ..."
-  cat ${KUBE_ROOT}/cluster/gce/configure-vm.sh | gcloud compute ssh --ssh-flag="-o LogLevel=quiet" --project "${PROJECT}" --zone "${ZONE}" "${node}" --command "sudo bash -s -- --push" &> ${OUTPUT}/push-"${node}".log
+  cat ${KUBE_TEMP}/configure-vm.sh | gcloud compute ssh --ssh-flag="-o LogLevel=quiet" --project "${PROJECT}" --zone "${ZONE}" "${node}" --command "sudo bash -s -- --push" &> ${OUTPUT}/push-"${node}".log
 }
 
 # Push binaries to kubernetes cluster
@@ -1354,3 +1356,8 @@ function ssh-to-node {
 function prepare-e2e() {
   detect-project
 }
+
+# Writes configure-vm.sh to a temporary location with comments stripped.
+function prepare-startup-script() {
+  sed '/^\s*#\([^!].*\)*$/ d' ${KUBE_ROOT}/cluster/gce/configure-vm.sh > ${KUBE_TEMP}/configure-vm.sh
+}