diff --git a/check/check-system-flags b/check/check-system-flags
index 632496c..e2e6633 100755
--- a/check/check-system-flags
+++ b/check/check-system-flags
@@ -34,10 +34,10 @@ PKG_CONFIG_SYSTEM_INCLUDE_PATH=/foo/include
 PKG_CONFIG_SYSTEM_LIBRARY_PATH=/foo/lib
 
 RESULT="-I/usr/include"
-run_test --cflags system
+PKG_CONFIG_ALLOW_SYSTEM_CFLAGS=1 run_test --cflags system
 
 RESULT="-L/usr/lib -lsystem"
-run_test --libs system
+PKG_CONFIG_ALLOW_SYSTEM_LIBS=1 run_test --libs system
 
 # Now check that the various GCC environment variables also update the
 # system include path
@@ -56,7 +56,7 @@ done
 # system include path when --msvc-syntax is in use
 for var in INCLUDE; do
     RESULT="-I/usr/include"
-    eval $var=/usr/include run_test --cflags system
+    eval PKG_CONFIG_ALLOW_SYSTEM_CFLAGS=1 $var=/usr/include run_test --cflags system
 
     # Make sure these are skipped in --msvc-syntax mode
     if [ "$native_win32" = yes ]; then