Syrian air defences intercepted at least two Israeli missiles fired at a government "military position" in Damascus province early Saturday but the attack still caused damage, state media reported.

The Syrian Observatory for Human Rights, a Britain-based monitor of the war, said the missiles, presumably Israeli, targeted "positions of the Syrian regime and its allies" southwest of Damascus.

An Israeli military spokesman declined to comment.

"At half past midnight (2230 GMT Friday), the Israeli enemy fired several surface-to-surface missiles at a military position in Damascus province," the state SANA news agency reported.

"The air defences of the Syrian army were able to deal with the attack... destroying two of the missiles," it said, adding that the attack nonetheless caused "material damage".

Observatory chief Rami Abdel Rahman said the missile strike targeted a military base near Kesweh, south of Damascus.

"An arms depot was destroyed," he said, adding that it was not immediately clear whether the warehouse was operated by the Syrian army, or its allies Iran or Lebanese militant group Hezbollah.

Israel has acknowledged carrying out repeated air and missile strikes in Syria since the outbreak of the bloody civil war six years ago to stop arms deliveries to Hezbollah, with which it fought a devastating 2006 conflict.

It has also systematically targeted government positions in response to all fire into territory under its control, whoever launched it and regardless of whether it was intentional or not.

Israel seized 1,200 square kilometres (460 square miles) of the Golan Heights from Syria in the Six-Day War of 1967 and later annexed it in a move never recognised by the international community.

The two countries remain technically at war.