diff --git a/lib/setuplib.php b/lib/setuplib.php
index c206d10fb68..cc1cd12030d 100644
--- a/lib/setuplib.php
+++ b/lib/setuplib.php
@@ -1193,7 +1193,12 @@ function make_upload_directory($directory, $exceptiononerror = true) {
  */
 function make_temp_directory($directory, $exceptiononerror = true) {
     global $CFG;
-    protect_directory($CFG->tempdir);
+    if ($CFG->tempdir !== "$CFG->dataroot/temp") {
+        check_dir_exists($CFG->tempdir, true, true);
+        protect_directory($CFG->tempdir);
+    } else {
+        protect_directory($CFG->dataroot);
+    }
     return make_writable_directory("$CFG->tempdir/$directory", $exceptiononerror);
 }
 
@@ -1206,7 +1211,12 @@ function make_temp_directory($directory, $exceptiononerror = true) {
  */
 function make_cache_directory($directory, $exceptiononerror = true) {
     global $CFG;
-    protect_directory($CFG->cachedir);
+    if ($CFG->cachedir !== "$CFG->dataroot/cache") {
+        check_dir_exists($CFG->cachedir, true, true);
+        protect_directory($CFG->cachedir);
+    } else {
+        protect_directory($CFG->dataroot);
+    }
     return make_writable_directory("$CFG->cachedir/$directory", $exceptiononerror);
 }