diff --git a/scripts/CMakeLists.txt b/scripts/CMakeLists.txt
index 84472c3a5c3..be25386c68f 100644
--- a/scripts/CMakeLists.txt
+++ b/scripts/CMakeLists.txt
@@ -91,16 +91,18 @@ ENDIF()
 
 IF(CMAKE_GENERATOR MATCHES "Makefiles")
   # No multiconfig build - use CMAKE_C_FLAGS
-  SET(CFLAGS "@CMAKE_C_FLAGS@")
-  SET(CXXFLAGS "@CMAKE_CXX_FLAGS@")
+  # Strip maintainer mode options if necessary
+  STRING(REPLACE "${MY_MAINTAINER_C_WARNINGS}" "" CFLAGS "${CMAKE_C_FLAGS}")
+  STRING(REPLACE "${MY_MAINTAINER_CXX_WARNINGS}" "" CXXFLAGS "${CMAKE_CXX_FLAGS}")
   FOREACH(ARCH ${CMAKE_OSX_ARCHITECTURES})
     SET(CFLAGS   "${CFLAGS} -arch ${ARCH}")
     SET(CXXFLAGS "${CXXFLAGS} -arch ${ARCH}")
   ENDFOREACH()
 ELSE()
   # Multiconfig build - use CMAKE_C_FLAGS_RELWITHDEBINFO
-  SET(CFLAGS "@CMAKE_C_FLAGS_RELWITHDEBINFO@")
-  SET(CXXFLAGS "@CMAKE_CXX_FLAGS_RELWITHDEBINFO@")
+  # Strip maintainer mode options if necessary
+  STRING(REPLACE "${MY_MAINTAINER_C_WARNINGS}" "" CFLAGS "${CMAKE_C_FLAGS_RELWITHDEBINFO}")
+  STRING(REPLACE "${MY_MAINTAINER_CXX_WARNINGS}" "" CXXFLAGS "${CMAKE_CXX_FLAGS_RELWITHDEBINFO}")
 ENDIF()
 
 IF(UNIX)