diff --git a/bootstrap/bootstrap_storage.sh b/bootstrap/bootstrap_storage.sh
index 323cc528c435..7aafb9692cb6 100755
--- a/bootstrap/bootstrap_storage.sh
+++ b/bootstrap/bootstrap_storage.sh
@@ -33,7 +33,6 @@ done
 
 BOOTSTRAP_DIR=`dirname ${PRG}`
 CONFIG_FILE_PATH=${BOOTSTRAP_DIR}/../conf/openmetadata.yaml
-FLYWAY_SQL_ROOT_DIR="${BOOTSTRAP_DIR}/sql/migrations/flyway"
 NATIVE_SQL_ROOT_DIR="${BOOTSTRAP_DIR}/sql/migrations/native"
 
 # Which java to use
@@ -61,7 +60,7 @@ execute() {
   if  [ ${debug} ] ; then
     echo "Using Configuration file: ${CONFIG_FILE_PATH}"
   fi
-  ${JAVA} -Dbootstrap.dir=$BOOTSTRAP_DIR  -cp ${CLASSPATH} ${TABLE_INITIALIZER_MAIN_CLASS} -c ${CONFIG_FILE_PATH} -s ${FLYWAY_SQL_ROOT_DIR} -n ${NATIVE_SQL_ROOT_DIR} --${1} -force ${force}  -${debug}
+  ${JAVA} -Dbootstrap.dir=$BOOTSTRAP_DIR  -cp ${CLASSPATH} ${TABLE_INITIALIZER_MAIN_CLASS} -c ${CONFIG_FILE_PATH} --${1} -force ${force}  -${debug}
 }
 
 printUsage() {
diff --git a/openmetadata-service/src/main/java/org/openmetadata/service/util/TablesInitializer.java b/openmetadata-service/src/main/java/org/openmetadata/service/util/TablesInitializer.java
index ee677eff30bb..bd8a9d8cc5aa 100644
--- a/openmetadata-service/src/main/java/org/openmetadata/service/util/TablesInitializer.java
+++ b/openmetadata-service/src/main/java/org/openmetadata/service/util/TablesInitializer.java
@@ -70,10 +70,6 @@ public final class TablesInitializer {
   static {
     OPTIONS = new Options();
     OPTIONS.addOption("debug", DEBUG_MODE_ENABLED, false, "Enable Debug Mode");
-    OPTIONS.addOption("s", OPTION_FLYWAY_SCRIPT_ROOT_PATH, true, "Root directory of flyway sql script path");
-    OPTIONS.addOption("n", OPTION_NATIVE_SQL_ROOT_PATH, true, "Root directory of native sql script path");
-    OPTIONS.addOption("e", OPTION_EXTENSION_SQL_ROOT_PATH, true, "Root directory for extension migrations to execute");
-
     OPTIONS.addOption("c", OPTION_CONFIG_FILE_PATH, true, "Config file path");
     OPTIONS.addOption(
         OPTION_FORCE_MIGRATIONS,
@@ -119,12 +115,6 @@ private TablesInitializer() {}
   public static void main(String[] args) throws Exception {
     CommandLineParser parser = new DefaultParser();
     CommandLine commandLine = parser.parse(OPTIONS, args);
-    if (!commandLine.hasOption(OPTION_CONFIG_FILE_PATH)
-        || !commandLine.hasOption(OPTION_NATIVE_SQL_ROOT_PATH)
-        || !commandLine.hasOption(OPTION_FLYWAY_SCRIPT_ROOT_PATH)) {
-      usage();
-      System.exit(1);
-    }
     if (commandLine.hasOption(DEBUG_MODE_ENABLED)) {
       debugMode = true;
     }
@@ -204,15 +194,15 @@ public static void main(String[] args) throws Exception {
     if (disableValidateOnMigrate) {
       printToConsoleInDebug("Disabling validation on schema migrate");
     }
-    String nativeSQLScriptRootPath = commandLine.getOptionValue(OPTION_NATIVE_SQL_ROOT_PATH);
-    String scriptRootPath = commandLine.getOptionValue(OPTION_FLYWAY_SCRIPT_ROOT_PATH);
-    String extensionSQLScriptRootPath = commandLine.getOptionValue(OPTION_EXTENSION_SQL_ROOT_PATH);
+    String nativeSQLScriptRootPath = config.getMigrationConfiguration().getNativePath();
+    String flywayRootPath = config.getMigrationConfiguration().getFlywayPath();
+    String extensionSQLScriptRootPath = config.getMigrationConfiguration().getExtensionPath();
     Flyway flyway =
         get(
             jdbcUrl,
             user,
             password,
-            scriptRootPath,
+            flywayRootPath,
             config.getDataSourceFactory().getDriverClass(),
             !disableValidateOnMigrate);
     try {