Warplanes hit the port's container yard, causing a number of containers to catch fire but without causing casualties, local media say.
Israeli warplanes fired missiles on the port of the coastal city of Latakia without inflicting any human losses, the Syrian regime has said.
The regime media quoted an unnamed military official as saying that early on Tuesday several missiles struck the area of the containers in the port setting some of them on fire.
"Around 1:23 am today (2323 GMT), the Israeli enemy carried out an air aggression with several missiles," SANA news agency quoted a military source as saying.
"Our air defences repelled the Israeli aggression in Latakia."
It was a rare attack on the port of Latakia, a vital facility where much of Syria's imports are brought into the war-torn country.
Syrian regime media reported that five explosions were heard in the port and a huge fire erupted in the containers area and fire engines have rushed to the port.
There was no comment from the Israeli military.
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Israel rarely acknowledges strikes
Israel has staged hundreds of strikes on targets inside regime-controlled Syria over the years but rarely acknowledges or discusses such operations.
Some of the strikes in the past had targeted the main airport in the capital Damascus.
However, Israel has acknowledged that it targets Iran-allied militias such as Lebanon's Hezbollah, which has deployed fighters within Syria.
Israel says Iranian presence on its northern frontier is a red line, justifying its strikes on facilities and weapons inside Syria.