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"This action by the dhow's crew demonstrated hostile intent which resulted in the defensive fire by the Coast Guardsmen," he said.
Dhows are traditional wooden boats common to the region that are typically used for trade.
No Americans were wounded in the encounter, which happened in international waters around 11:30 a.m. local time Tuesday, Stephens said.
The Monomoy was operating on "a routine maritime security operation" when it contacted the dhow's bridge. After initial contact, the Iranian vessel stopped communicating and the Coast Guard ship deployed small boat to investigate, Stephens said.
It was not clear if the shot hit the Iranian vessel or if anyone onboard was injured. Iranian officials could not immediately be reached for comment.
American, Iranian and other countries' military vessels routinely patrol the Gulf, a key route for international oil shipments, usually without incident.
Speed boats from Iran's Revolutionary Guard, however, have passed close to U.S. ships in incidents that have raised alarm in Washington.
In early 2008, then-President George W. Bush accused Iran of a "provocative act" after five small Iranian craft buzzed around the destroyer USS Hopper.
Tuesday's encounter happened as the U.S. and other world powers negotiate with Iran over its controversial nuclear program, and just days after Iran claimed it shot down a purported Israeli drone near a nuclear facility. Israeli officials have not commented on that incident.
The West and Israel believe the program is aimed at building a nuclear weapon. Iran denies the charge, saying its nuclear activities are for peaceful purposes only, such as power generation and medical research.
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