The incident was condemned by US security forces who said Iran had been acting increasingly provocatively and unpredictably in recent months.
Despite being in international waters in the Strait of Hormuz, the American ships were aggressively approached by members of the Iranian Navy on Tuesday.
Iranian forces trained their weapons on the US flotilla, which was made up of five ships and included the huge aircraft carrier USS George H.W. Bush.
In response, America deployed helicopters from the warship to hover over the small attack ships.
Washington said the helicopters were then also threatened.
Rear Admiral Kenneth Whitesell, commander of the Carrier Strike Group 2, said Iran had been unnecessarily aggressive during the incident.
Iran said the US ships had breached its territory – a claim America denies.
Rear Admiral Whitesell said: “What I don’t like about that is they were in the middle of international transit waters. We had a right to be there as we were exercising freedom of navigation on our way into the Arabian Gulf.
“They also had weapons uncovered as some of the cameras were able to tell. They had some of the weapons manned. We also have aerial data that they were arming all of these weapons.”
Captain Will Pennington, commanding officer on the aircraft carrier, said Iran had shown “certainly unprofessional behaviour”.
He added they had been acting in a “more aggressive and less predictable” manner in recent months, as tensions continue to escalate between the Middle Eastern country and the West.
Earlier this month, Iranian attack ships came threateningly close to British Royal Navy vessels, forcing them to change route to avoid a disastrous collision.
US officials revealed the Iranian Revolutionary Guard Corps had ignored calls to change their course, eventually coming within 600 yards of the British ships.
And in February, America put Iran “on notice” following a controversial missile test.
Security advisor Michael Flynn said: “As of today, we are officially putting Iran on notice.
“The Obama administration failed to respond adequately to Tehran’s malign actions — including weapons transfers, support for terrorism and other violations of international norms.”