diff --git a/configure/RULES_TOP b/configure/RULES_TOP
index b18fbf026..bd844e76f 100644
--- a/configure/RULES_TOP
+++ b/configure/RULES_TOP
@@ -26,8 +26,10 @@ realuninstall: uninstallDirs
 UNINSTALL_DIRS += $(INSTALL_DBD) $(INSTALL_INCLUDE) $(INSTALL_DOC) \
     $(INSTALL_HTML) $(INSTALL_TEMPLATES) $(INSTALL_DB) $(DIRECTORY_TARGETS)
 ifneq ($(INSTALL_LOCATION),$(TOP))
+ifneq ($(INSTALL_LOCATION),$(EPICS_BASE))
 UNINSTALL_DIRS += $(INSTALL_CONFIG)
 endif
+endif
 uninstallDirs:
 	$(RMDIR) $(UNINSTALL_DIRS)