The official said the USS Thunderbolt fired the warning shots after attempts to communicate by radio were ignored by the Iranian vessel. The action was described by the USA military as "unsafe and unprofessional".
FOX News has updating details, including the last time a U.S. Navy warship fired warning shots at an Iranian vessel which approached too close.
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However, tensions remain over the Syrian war and Iran's ballistic missile programme, and stand-offs at sea have happened.
The Trump administration, which has struck a hard line on Iran, recently declared that Iran was complying with its nuclear agreement with world powers, but warned that Tehran was not following the spirit of the accord and that Washington would look for ways to strengthen it.
While the number of encounters between Iranian and USA forces has declined in recent months, Tuesday's incident is one of several so far this year.
Such incidents occur occasionally. An armed vessel belonging to Iran's elite Islamic Revolutionary Guards Corps came within 150 yards of the Thunderbolt as it conducted training exercises in global waters, according to defense officials.
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