diff --git a/eclass/autotools.eclass b/eclass/autotools.eclass
index 9143aa454d0d..0546c5c3c576 100644
--- a/eclass/autotools.eclass
+++ b/eclass/autotools.eclass
@@ -518,6 +518,31 @@ autotools_run_tool() {
 		set -- "${1}" $(autotools_m4dir_include) "${@:2}" $(autotools_m4sysdir_include)
 	fi
 
+	# re-order arguments, bug #680210
+	local _old_args=( ${@} )
+	local _at_command=
+	local _at_file=
+	local -a _at_args=()
+	local _argument=
+
+	for _argument in ${_old_args[*]}; do
+		if [[ -z "${_at_command}" ]]; then
+			_at_command=${_argument}
+			continue
+		fi
+
+		if [[ -z "${_at_file}" && "${_argument}" =~ \.(in|ac)$ ]]; then
+			_at_file=${_argument}
+			continue
+		fi
+
+		_at_args+=( ${_argument} )
+	done
+
+	debug-print "\$@ before reordering of arguments: ${@}"
+	set -- "${_at_command}" "${_at_args[@]}" "${_at_file}"
+	debug-print "\$@ after reordering of arguments: ${@}"
+
 	# If the caller wants to probe something, then let them do it directly.
 	if ${return_output} ; then
 		"$@"