Israeli warplanes hit a weapons shipment in Syria headed for Lebanon's Hezbollah, media quoted US officials as saying, with a diplomatic source reporting Saturday that the strikes targeted missiles stored at Damascus airport.
Activists, meanwhile, said the bodies of 62 civilians, including children, were found in the northwest port of Banias a day after an assault by regime troops and the opposition Syrian National Coalition warned against what it called "ethnic cleansing."
CNN said US and Western intelligence agencies were reviewing information suggesting Israel had launched an air strike overnight on Thursday.
Washington does not believe Israeli warplanes entered Syrian airspace during the raid, it added.
US President Barack Obama, speaking to Spanish-language Telemundo television, said Israel is justified in protecting itself against arms shipments to Hezbollah.
"The Israelis justifiably have to guard against the transfer of advanced weaponry to terrorist organisations like Hezbollah," he said, without commenting directly on the reported strike.
"We coordinate closely with the Israelis, recognising that they are very close to Syria, they are very close to Lebanon."
Lebanon's military said pairs of Israeli aircraft entered their airspace three times on Thursday night and stayed for two to three hours at a time.
NBC cited US officials as saying the primary target was believed to be a weapons shipment headed for Hezbollah, the Lebanese Shiite group closely allied with President Bashar al-Assad's regime.
One said the raid was probably tied to delivery systems for chemical weapons, but CNN cited officials as saying there was no reason to believe Israel had struck chemical weapons storage facilities.
A Syrian military source denied the raid had taken place at all, and an Israeli defence official would say only the Jewish state "was following the situation in Syria and Lebanon, with an emphasis on transferring chemical weapons and special arms".
But a diplomatic source in Lebanon told AFP the operation destroyed surface-to-air missiles recently delivered by Russia that were being stored at Damascus airport.
On Friday, Syrian state news agency SANA reported that rebels had fired two rockets at the airport at dawn, hitting a kerosene tank.
If confirmed, the raid would mark the second time Israel has hit Syria this year after it implicitly admitted a January strike on arms thought to be en route to Hezbollah.
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The Syrian Observatory for Human Rights said the 62 bodies found in Banias were those of civilians killed by the army on Friday, and warned the toll could rise.
"We have identified 62 citizens by their names, photos, or videos, including 14 children, and the number could rise because there are dozens of citizens who are still missing," a statement said.
The opposition Coalition condemned "a proliferation of massacres that is transforming into an ethnic cleansing operation like that carried out by Serbian forces in Bosnia 20 years ago."
The Observatory has said at least 50 people had been killed in the Sunni village of Bayda, just south of Banias, on Thursday.
"Some were summarily executed, shot to death, stabbed or set on fire," it said.
On Saturday, Washington said it was "appalled" by the reported killings in Bayda.
Another 10 people were killed in the Banias district of Ras al-Nabaa on Friday, the Observatory said, distributing grisly footage of dead bodies, including those of children.
The reported killings triggered panic in the Banias region.
"Hundreds of families are fleeing Sunni neighbourhoods in Banias in fear of a new massacre," Observatory chief Rami Abdel Rahman said earlier.
Elsewhere, regime forces and Hezbollah fighters advanced towards the town of Qusayr in central Homs province, where at least 16 people were killed, the Observatory said.
With the violence mounting and pressure on Washington to arm Syria's outgunned rebels, Obama came close to ruling out deploying US troops to Syria.
"As a general rule, I don't rule things out as commander-in-chief because circumstances change," Obama said on Thursday in Costa Rica.
"Having said that, I do not foresee a scenario in which boots on the ground in Syria -- American boots on the ground in Syria -- would not only be good for America but also would be good for Syria."
Speculation has mounted that his administration could reverse its opposition to arming the rebels after the White House said last week Assad had probably used chemical weapons on his own people.
At least 70,000 people have been killed in Syria since March 2011, according to the UN, including at least 44 people on Saturday, according to a preliminary Observatory toll.