The Israeli raid "directly targeted an Iranian weapons shipment in the container yard," the Syrian Observatory for Human Rights said.
Syrian state media reported the strike on the container yard at Latakia port without specifying what was targeted.
The Observatory, a UK-based organisation with a wide network of sources on the ground across Syria, said the raid triggered a series of explosions.
It reported "huge material losses" but added there were no immediate reports of casualties.
According to the Syrian state news agency SANA, the strike occurred at 1:23 am (2323 GMT Monday).
"Our air defences repelled the Israeli aggression in Latakia," it said, adding that a number of containers caught fire in the strike.
Latakia is the northernmost of Syria's main ports, and lies around 230 kilometres (140 miles) north of Damascus.
Photos and footage published by SANA showed a fire in the yard but state television said later that firefighters had brought the blaze under control.
For an optimal experience, please
