The July 5 strike failed to get all the Russian Yakhont supersonic anti-ship cruise missiles because some were removed from their launchers and warehouse before the attack, the officials told The New York Times.
But to make it look like Israel had dealt a devastating blow, the regime of President Bashar Assad set fire to the launchers and to vehicles at the destroyed warehouse to hide the fact the Yakhont missiles were missed, U.S. intelligence reports cited by the newspaper said.
The Pentagon had no immediate comment. Israel has a longstanding policy of not acknowledging pre-emptive military strikes. Damascus also had no immediate comment.
Israeli officials have said they will do what they believe they need to do to stop sophisticated weapons from falling into the hands of Hezbollah, the Lebanese Shiite Islamic militant group and political party whose manifesto calls for Israel's elimination.
U.S. and Israeli naval officials consider the advanced radar Yakhont missiles a serious threat to their ships.
The July 5 attack near the Mediterranean port city of Latakia was the fourth known Israeli airstrike in Syria this year.
U.S. officials told the Times Wednesday Israeli aircraft fired air-to-ground missiles at the warehouse from the eastern Mediterranean, never entering Syrian airspace.