It was initially reported that a US cargo ship had been shot at and boarded, but it later emerged the ship was the MV Maersk Tigris, a Danish owned vessel registered in the Marshall Islands.
The Pentagon said in a statement that Iranian forces boarded the ship at around 9am local time on Tuesday after firing a warning shot across its bows as it was traveling through the Strait of Hormuz. The Iranians then forced the ship deeper into Iranian waters.
“The master was contacted and directed to proceed further into Iranian territorial waters. He declined and one of the Revolutionary Guard Corps Navy (IRGCN) craft fired shots across the bridge of the Maersk Tigris,” said spokesman Col Steve Warren.
“The master complied with the Iranian demand and proceeded into Iranian waters in the vicinity of Larak Island.”
Mr Warren said that the US Navy responded to a distress call and dispatched a Navy Destroyer, USS Farragut to travel to the cargo ship as quickly as possible “to observe the interaction”.
He added: "[Navy Central Command] is communicating with representatives of the shipping company and we continue to monitor the situation. According to information received from the vessel's operators, there are no Americans aboard.”
The vessel has been directed to the Iranian port of Bandar Abbas on the southern coast, Al-Arabiya reported.
Iran's semi-official Fars news agency suggested that the ship was trespassing in the Persian Gulf.
Negotiators from the US and five other nations are attempting to secure an agreement by the end of June requiring Iran to curb its nuclear program in exchange for an easing of sanctions which has damaged the nation's economy.
This week, the US Senate will begin debating a bill allowing Congress to review the potential agreement.
EU foreign policy chief Federica Mogherini will on Tuesday meet with Iranian Foreign Minister Mohammad Javad Zarif in New York, for talks on Iran's nuclear programme and other issues, an EU official said.
However, it is not yet known whether the incident at sea will be addressed during the meeting.