Columns of fire were seen lighting up the sky after a series of blasts over several hours in locations around the Syrian capital. One eyewitness said: "Night turned into day".
Israel made no official comment but Syria accused the Jewish state of striking the Jamrya military facility north of Damascus, which was hit by Israeli jets three months ago.
If confirmed, the attack would be the second major operation in Syria within three days.
Video footage uploaded onto the Internet by anti-Assad activists showed a series of explosions. One lit up the skyline of Damascus while another sent up a tower of flames and secondary blasts.
A western intelligence source said that, as in two previous strikes attributed to Israel this year, the target was a shipment of Fateh missiles in transit from Iran to the Lebanese militant group Hezbollah.
The pro-opposition Syrian Observatory for Human Rights said the blasts hit Jamraya as well as a nearby ammunition depot.
Other activists said a missile brigade and two Republican Guard battalions may also have been targeted in the heavily militarised area just north of Damascus.
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