"The behaviour of the Guard navy is not very professional and not very supportive of peace in the Gulf area," Admiral Gary Roughead said at a news conference in Dubai.
In January, the United States said Iranian boats aggressively approached three U.S. naval ships and warned they would explode. Iran said it was a routine contact.
"I would like to see the Iranian Revolutionary Guard navy … more mindful of the importance of communicating not just with the U.S. Navy but with any other navy about intentions and movements," Roughead said.
Tension has been high between Washington and Iran in Gulf waters, which are vital to world oil shipments.
Relations were already tense over Iran's nuclear programme, which the Islamic Republic says is peaceful but the United States suspects is aimed at developing atomic weapons.
Another incident occurred this month, when three boats approached a U.S. Navy patrol vessel at high speed, stopping only after it fired a flare.
The Bahrain-based U.S. Fifth Fleet said at the time that the American vessel had tried to communicate with the boats by routine methods but decided to fire a flare after receiving no response.
The Iranian Revolutionary Guard, labelled by the U.S. Senate a terrorist organisation, patrols Gulf waters.
The Gulf is vital to world oil shipments, with about 17 million barrels per day of crude oil, more than one third of total global shipments, passing through the waterway.
"We see our presence (here) as enduring… the purpose is to ensure that a very important part of the world enjoys free flow of commerce," Roughead said. (Reporting by Ola Galal; Editing by Lin Noueihed and Andrew Dobbie)
