The official said the strike targeted Russian-made missiles intended for the Lebanese militant group Hezbollah.
Latakia is a stronghold of Syrian President Bashar al-Assad, an important port city where the Alawite community to which he belongs is concentrated.
Israel is widely reported to have carried out at least three air strikes in Syria so far this year.
While Israel rarely comments on specific operations, it has repeatedly said it would act if it felt Syrian weapons, conventional or chemical, were being transferred to militant groups in the region, especially Hezbollah.
Reports of the strike came as the Organization for the Prohibition of Chemical Weapons (OPCW) said all Syria’s declared equipment for making chemical weapons had been destroyed, one day before a deadline.
Action by the OPCW was agreed following allegations, denied by the Syrian government, that its forces had used chemical weapons in civilian areas – and after the US and France threatened military intervention.
A US official said the Israeli strike took place overnight from Wednesday into Thursday.
Reports circulated on Thursday of explosions near Latakia, but the cause was not clear.
“Several explosions were heard in an air defense base in the Snubar Jableh area,” said the Syrian Observatory for Human Rights, a UK-based activist network.
Neither Israel nor Syria have commented on the reports.
One unnamed US official told the Associated Press that the missiles targeted by Israel were Russian-made SA-125s.
Russia has been a key backer of President Bashar al-Assad’s, continuing to supply his government with weapons during the conflict in Syria.
Bashar al-Assad had promised to respond to any future strikes by Israel.
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