The US carrier was "unprofessional and provocative" Friday, the IRGC navy said in a statement Saturday.
CNN has asked the US Navy for a response.
The USS Nimitz and a second American ship dispatched a helicopter near an oil and gas platform and approached Iranian ships, the IRGC navy said.
Iranian vessels ignored the warning flares, and the American ships later left the area, the Iranian navy added.
This is the latest in a series of encounters involving the two navies.
On Tuesday, a US Navy ship fired warning shots at an armed Iranian patrol boat in the northern end of the Persian Gulf, according to two US defense officials.
The officials said the Iranian boat is believed to have been operated by the Islamic Revolutionary Guard Corps.
It approached and came within 150 yards of the USS Thunderbolt, a US Navy patrol ship.
The Navy ship fired warning shots into the water over concerns of a collision, one of the officials said.
Pentagon spokesman US Navy Capt. Jeff Davis previously told reporters that there had been 35 incidents of unsafe or unprofessional behavior by Iranian vessels in 2016, although the "vast majority" had occurred in the first half of that year.
In June, the US military labeled the actions of an Iranian vessel "unsafe and unprofessional" after it trained a laser on a US helicopter that was accompanying a formation of American ships transiting the international waters of the Strait of Hormuz.
No warning shots were fired during that encounter, but US defense officials criticized the use of the Iranian laser.
In April, the US accused a a guard corps ship of acting in an "unprofessional but also provocative" manner while approaching an American destroyer, the USS Mahan, while it was sailing in the Persian Gulf.