An alleged threat to blow up US warships "may not have come" from Iranian speedboats involved in a recent stand-off, the BBC has learned.
The voice on a Pentagon tape could instead have come from another ship in the area or a transmitter on land, senior US Navy sources told the BBC.
The US has sent Iran a formal protest over Sunday's stand-off in the Strait of Hormuz.
Iran has accused the US of faking its video of the incident.
Iranian state-run TV has broadcast a separate video of the stand-off, in which there is no sign of threatening behaviour by the Iranian patrols, thought to belong to the Revolutionary Guards.
But the four-minute clip does not appear to show the whole incident.
The US military said video and audio that it released confirmed its allegation that Iranian speedboats harassed US warships and threatened to blow them up in a radio communication.
"I am coming at you. You will explode in a couple of minutes," the Iranians said in a radio transmission, according to US officials.
Pentagon officials said the speedboats came within about 200m (650ft) of the US vessels.
US officials have described the actions of the speed boats as dangerous and provocative.
US sailors assumed battle stations and the captain on one of the ships was about to order an attack when the Iranian boats turned away, they said.
On Wednesday the US lodged a formal diplomatic complaint with the Iranian foreign ministry through the Swiss embassy in Tehran.
The New York Times noted on Wednesday that the US-released audio includes no ambient noise of the kind that might be expected if the broadcast had come from on one of the speedboats.
Pentagon officials said the voice heard in the video clip is not directly traceable to the Iranian military, but could still have come from a high quality radio on one of the small boats, the paper reported.
Iran described the incident as a routine contact which happens all the time in the crowded waters of the Gulf.
The Pentagon has insisted that the three US vessels - identified as navy cruiser USS Port Royal, destroyer USS Hopper and frigate USS Ingraham - were in international waters.
The confrontation has further inflamed tensions between arch-foes Iran and the United States.
US President George W Bush is currently on a tour of the Middle East which will tackle what the Americans see as the threat posed by Iran to regional stability.