diff --git a/test/build.sh b/test/build.sh
index 2e608598..8cab8509 100755
--- a/test/build.sh
+++ b/test/build.sh
@@ -26,15 +26,33 @@ NPD_STAGING_PATH=${NPD_STAGING_PATH:-"gs://node-problem-detector-staging"}
 NPD_STAGING_REGISTRY=${NPD_STAGING_REGISTRY:-"gcr.io/node-problem-detector-staging"}
 PR_ENV_FILENAME=${PR_ENV_FILENAME:-"pr.env"}
 CI_ENV_FILENAME=${CI_ENV_FILENAME:-"ci.env"}
+CI_CUSTOM_FLAGS_ENV_FILENAME=${CI_CUSTOM_FLAGS_ENV_FILENAME:-"ci-custom-flags.env"}
 ROOT_PATH=$(git rev-parse --show-toplevel)
 GCS_URL_PREFIX="https://storage.googleapis.com/"
 
+
 function print-help() {
-  echo "Usage: build.sh [args...]"
-  echo "Available arguments:"
-  echo "  pr [pull_number]: Build node-problem-detector for presubmit jobs and push to staging."
-  echo "  ci:               Build node-problem-detector for CI jobs and push to staging."
-  echo "  get-ci-env:       Download environment variable file from staging for CI job."
+  echo "Usage: build.sh [flags] [command]"
+  echo
+  echo "Available flags:"
+  echo "  -p [PR_NUMBER]      Specify the pull request number when building for a presubmit job."
+  echo "  -f                  Use custom flags."
+  echo
+  echo "Available commands:"
+  echo "  help           Print this help message"
+  echo "  pr             Build node-problem-detector for presubmit jobs and push to staging. Flag -p is required."
+  echo "  ci             Build node-problem-detector for CI jobs and push to staging."
+  echo "  get-ci-env     Download environment variable file from staging for CI job."
+  echo "  install-lib    Install the libraries needed."
+  echo
+  echo "Examples:"
+  echo "  build.sh help"
+  echo "  build.sh -p [PR_NUMBER] pr"
+  echo "  build.sh -p [PR_NUMBER] -f pr"
+  echo "  build.sh ci"
+  echo "  build.sh get-ci-env"
+  echo "  build.sh -f get-ci-env"
+  echo "  build.sh install-lib"
 }
 
 function get-version() {
@@ -65,17 +83,43 @@ export NODE_PROBLEM_DETECTOR_TAR_HASH=$(sha1sum ${ROOT_PATH}/node-problem-detect
 export EXTRA_ENVS=NODE_PROBLEM_DETECTOR_IMAGE=${REGISTRY}/node-problem-detector:${TAG}
 EOF
 
+  if [[ -n "${NODE_PROBLEM_DETECTOR_CUSTOM_FLAGS:-}" ]]; then
+    cat >> ${ROOT_PATH}/${env_file} <<EOF
+export NODE_PROBLEM_DETECTOR_CUSTOM_FLAGS="${NODE_PROBLEM_DETECTOR_CUSTOM_FLAGS}"
+EOF
+  fi
+
   echo "Written env file ${ROOT_PATH}/${env_file}:"
   cat ${ROOT_PATH}/${env_file}
 }
 
+function build-npd-custom-flags() {
+  local -r kube_home="/home/kubernetes"
+
+  local -r km_config="${kube_home}/node-problem-detector/config/kernel-monitor.json"
+  local -r dm_config="${kube_home}/node-problem-detector/config/docker-monitor.json"
+  local -r sm_config="${kube_home}/node-problem-detector/config/systemd-monitor.json"
+
+  local -r custom_km_config="${kube_home}/node-problem-detector/config/kernel-monitor-counter.json"
+  local -r custom_dm_config="${kube_home}/node-problem-detector/config/docker-monitor-counter.json"
+  local -r custom_sm_config="${kube_home}/node-problem-detector/config/systemd-monitor-counter.json"
+
+  flags="--v=2"
+  flags+=" --logtostderr"
+  flags+=" --system-log-monitors=${km_config},${dm_config},${sm_config}"
+  flags+=" --custom-plugin-monitors=${custom_km_config},${custom_dm_config},${custom_sm_config}"
+  flags+=" --port=20256"
+
+  export NODE_PROBLEM_DETECTOR_CUSTOM_FLAGS=${flags}
+}
+
 function build-pr() {
-  local -r PR_NUMBER="${1}"
   if [[ -z "${PR_NUMBER}" ]]; then
-    echo "ERROR: pull_number is missing."
+    echo "ERROR: PR_NUMBER is missing."
     print-help
     exit 1
   fi
+
   # Use the PR number and current time as the name, e.g., pr261-20190314.224907.862195792
   local -r PR="pr${PR_NUMBER}-$(date +%Y%m%d.%H%M%S.%N)"
   echo "Building for PR ${PR}..."
@@ -96,42 +140,61 @@ function build-ci() {
   export VERSION="$(get-version)-$(date +%Y%m%d.%H%M)"
   export TAG="${VERSION}"
   make push
+
+  # Create the env file with and without custom flags at the same time.
+  build-npd-custom-flags
+  write-env-file ${CI_CUSTOM_FLAGS_ENV_FILENAME}
+  gsutil mv ${ROOT_PATH}/${CI_CUSTOM_FLAGS_ENV_FILENAME} ${UPLOAD_PATH}
+
+  export NODE_PROBLEM_DETECTOR_CUSTOM_FLAGS=""
   write-env-file ${CI_ENV_FILENAME}
   gsutil mv ${ROOT_PATH}/${CI_ENV_FILENAME} ${UPLOAD_PATH}
 }
 
 function get-ci-env() {
-  gsutil cp ${NPD_STAGING_PATH}/ci/${CI_ENV_FILENAME} ${ROOT_PATH}/${CI_ENV_FILENAME}
+  if [[ "${USE_CUSTOM_FLAGS}" == "true" ]]; then
+    gsutil cp ${NPD_STAGING_PATH}/ci/${CI_CUSTOM_FLAGS_ENV_FILENAME} ${ROOT_PATH}/${CI_CUSTOM_FLAGS_ENV_FILENAME}
+    echo "Using env file ${ROOT_PATH}/${CI_CUSTOM_FLAGS_ENV_FILENAME}:"
+    cat ${ROOT_PATH}/${CI_CUSTOM_FLAGS_ENV_FILENAME}
+  else
+    gsutil cp ${NPD_STAGING_PATH}/ci/${CI_ENV_FILENAME} ${ROOT_PATH}/${CI_ENV_FILENAME}
+    echo "Using env file ${ROOT_PATH}/${CI_ENV_FILENAME}:"
+    cat ${ROOT_PATH}/${CI_ENV_FILENAME}
+  fi
+}
 
-  echo "Using env file ${ROOT_PATH}/${CI_ENV_FILENAME}:"
-  cat ${ROOT_PATH}/${CI_ENV_FILENAME}
+main() {
+  cd ${ROOT_PATH}
+
+  if [[ "${USE_CUSTOM_FLAGS}" == "true" ]]; then
+    build-npd-custom-flags
+  fi
+
+  # This is for the deprecated usage: build.sh pr [PR_NUMBER]
+  if [[ -z "${PR_NUMBER}" ]]; then
+    PR_NUMBER="${2:-}"
+  fi
+
+  case ${1:-} in
+  help) print-help;;
+  pr) build-pr;;
+  ci) build-ci;;
+  get-ci-env) get-ci-env;;
+  install-lib) install-lib;;
+  *) print-help;;
+  esac
 }
 
 
-cd ${ROOT_PATH}
+USE_CUSTOM_FLAGS="false"
+PR_NUMBER=""
 
-if [[ "$#" -ne 1 && "$#" -ne 2 ]]; then
-  echo "ERROR: Illegal number of parameters."
-  print-help
-  exit 1
-fi
-COMMAND="${1}"
+while getopts "fp:" opt; do
+  case ${opt} in
+    f) USE_CUSTOM_FLAGS="true";;
+    p) PR_NUMBER="${OPTARG}";;
+  esac
+done
+shift "$((OPTIND-1))"
 
-if [[ "${COMMAND}" == "pr" ]]; then
-  if [[ "$#" -ne 2 ]]; then
-    echo "ERROR: pull_number is missing."
-    print-help
-    exit 1
-  fi
-  build-pr "${2}"
-elif [[ "${COMMAND}" == "ci" ]]; then
-  build-ci
-elif [[ "${COMMAND}" == "get-ci-env" ]]; then
-  get-ci-env
-elif [[ "${COMMAND}" == "install-lib" ]]; then
-  install-lib
-else
-  echo "ERROR: Invalid command."
-  print-help
-  exit 1
-fi
+main "$@"