diff --git a/pkgs/development/tools/misc/autogen/default.nix b/pkgs/development/tools/misc/autogen/default.nix
index 71ea938ea78f..623c9262ba3c 100644
--- a/pkgs/development/tools/misc/autogen/default.nix
+++ b/pkgs/development/tools/misc/autogen/default.nix
@@ -16,6 +16,9 @@ stdenv.mkDerivation rec {
     # Fix a broken sed expression used for detecting the minor
     # version of guile we are using
     sed -i "s,sed '.*-I.*',sed 's/\\\(^\\\| \\\)-I/\\\1/g',g" configure
+
+    # Don't write temporary files outside the build directory
+    sed -i "s,/tmp/mklibsrc-log.tx,$TMPDIR/mklibsrc-log.tx,g" pkg/libopts/mklibsrc.sh
   '';
 
   #doCheck = true; # 2 tests fail because of missing /dev/tty