diff --git a/usr.sbin/autofs/automount.c b/usr.sbin/autofs/automount.c
--- a/usr.sbin/autofs/automount.c
+++ b/usr.sbin/autofs/automount.c
@@ -260,6 +260,7 @@
 flush_caches(void)
 {
 	struct statfs *mntbuf;
+	struct statfs statbuf;
 	int i, nitems;
 
 	nitems = getmntinfo(&mntbuf, MNT_WAIT);
@@ -274,6 +275,21 @@
 			    mntbuf[i].f_mntonname);
 			continue;
 		}
+		/*
+		 * A direct map mountpoint may have been mounted over, in
+		 * which case we can't MNT_UPDATE it. There's an obvious race
+		 * condition remaining here, but that has to be fixed in the
+		 * kernel.
+		 */
+		if (statfs(mntbuf[i].f_mntonname, &statbuf) != 0) {
+			log_err(1, "cannot statfs %s", mntbuf[i].f_mntonname);
+			continue;
+		}
+		if (strcmp(statbuf.f_fstypename, "autofs") != 0) {
+			log_debugx("skipping %s, filesystem type is not autofs",
+			    mntbuf[i].f_mntonname);
+			continue;
+		}
 
 		flush_autofs(mntbuf[i].f_mntonname);
 	}