The USS Whidbey Island fired the warning shots on Dec. 19 in response to a small Iranian boat that was rapidly approaching it, said a U.S. Navy official.
"One small (Iranian) craft was coming toward it, and it stopped after the Whidbey Island fired warning shots," said the official, speaking on condition of anonymity because of the sensitivity of the issue.
It was the first official confirmation that the United States had fired warning shots in any recent confrontation with Iran in the Gulf.
In the second incident that month, the USS Carr encountered three small Iranian craft on Dec. 22, two of which were armed, said the official. The USS Carr did not fire warning shots, but sent warning blasts on the ships whistle, which caused the boats to turn around.
The official could not confirm whether the craft in either incident belonged to the Iranian Revolutionary Guards, the elite military force whose boats.
The top U.S. military commander in the Mideast said Friday that Iran runs the risk of triggering an unintended conflict if its boats continue to harass U.S. warships in the strait.
Adm. William J. Fallon, chief of U.S. Central Command, also said a threatening radio call heard during Sunday's encounter was likely connected to the Iranian vessels' provocative actions. He said the exact origin of the message was still unknown.
"This kind of behavior, if it happens in the future, is the kind of event that could precipitate a mistake," said Fallon. "If the boats come closer, at what point does the captain think it is a direct threat to the ship and has to do something to stop it?"
Iran has tried to downplay Sunday's incident as a normal occurrence, but U.S. officials have said that five Revolutionary Guards boats charged three U.S. Navy ships in a threatening manner, dropping boxes in the water in an apparent attempt to intimidate the Americans. The confrontation occurred just days before U.S. President W. Bush was scheduled to begin his first major Mideast trip.
The Pentagon has released a video of Sunday's incident, showing small Iranian boats swarming around U.S. warships in the Strait of Hormuz. In the recording, a man threatens in accented English, "I am coming to you. ... You will explode after ... minutes."
Fallon said Friday that the U.S. was still trying to determine the source of the threatening radio call but remained convinced that it was related to the actions of the Iranian boats.
"The voice is very strange. I don't know whether it came from the boats or one of the shore stations," he said in a telephone interview from Central Command headquarters in Florida. "But the timing of it is pretty suspicious. In my mind it is related to the maneuvers."
"It certainly doesn't sound like a third party that just happened to say something threatening at that moment," he added.
The radio call was heard over an open frequency often used by mariners to identify themselves and avoid accidents.
Iran has denied that its boats threatened the U.S. vessels and accused Washington of fabricating the video. Tehran has released its own video of the incident, which appeared to be shot from a small boat bobbing at least 100 yards from the American warships.
The footage does not shown any Iranian boats approaching the U.S. vessels or any provocation, and does not include threatening radio call. U.S. officials have said the controversial parts had been edited out of the Iranian video.
U.S. Navy and Iranian officials have said in the past that vessels from the two rival nations frequently come into contact in the waters of the narrow, heavily trafficked Gulf. They often communicate by radio to avoid incidents.
But the latest incident was the first time U.S. officials have spoken of such a direct threat from Iranian boats.
By Sebastian Abbot