The Pentagon said the incident was serious. It described the Iranian actions as "careless, reckless and potentially hostile" and said Tehran should provide an explanation.
In Tehran, the Iranian foreign ministry described the incident as ordinary.
"The example that happened on Saturday was similar to previous cases and is an ordinary and natural issue," Foreign Ministry spokesman Mohammad Ali Hosseini told Iran's official IRNA news agency.
"This is an ordinary issue that happens for the two sides every once in a while and, after the identification of the two sides, the issue is resolved."
The incident was the latest sign of tension between Washington and Tehran, at odds over a range of issues from Iran's nuclear programme to U.S. allegations of Iranian support for terrorism.
U.S. President George W. Bush is due to travel to the Middle East this week on a trip he has said is partly aimed at countering Iranian influence.
"We urge the Iranians to refrain from such provocative actions that could lead to a dangerous incident in the future," White House spokesman Gordon Johndroe said.
Oil prices briefly rose on the news about the confrontation as dealers weighed the threat to oil shipments along the key shipping route. Crude futures jumped 49 cents to $98.40 a barrel before slipping back.
In March, Iran seized 15 British sailors and marines in the Gulf and accused them of trespassing in Iranian territory while they inspected a merchant vessel. London maintained the British personnel were in Iraqi waters.
The British personnel were held for almost two weeks before being freed in what Iranian President Mahmoud Ahmadinejad said was a "gift" to the British people.
