diff --git a/Makefile.in b/Makefile.in
index ab2cc05f2ed..1fd5463dd2b 100644
--- a/Makefile.in
+++ b/Makefile.in
@@ -245,8 +245,8 @@ endif
 
 $(srcdir)/%/.git:
 	cd $(srcdir) && \
-	flock $(srcdir)/.git/config git submodule init $(dir $@) && \
-	flock $(srcdir)/.git/config git submodule update $(dir $@)
+	flock `git rev-parse --git-dir`/config git submodule init $(dir $@) && \
+	flock `git rev-parse --git-dir`/config git submodule update $(dir $@)
 
 #
 # GLIBC