Formed in January, the 412-strong Iraqi Coastal Defence Force (ICDF) has been trained by British, Australian, US and Dutch troops.
"Iraqis have taken responsibility for protecting territorial waters today, and actual work will begin tomorrow," Colonel Hameed Balafam, commander of the ICDF, said in a statement.
The fledgling navy set sail at a ceremony to mark its launch in the southern port of Umm Qasr, which was attended by Iraqi and US-led military officials.
It will be in charge of protecting a majority of the country's all-important oil exports which have been the target of a spate of devastating sabotage attacks in recent months, the statement said.
"Our first mission will be to protect oil ports in Basra and Khor al-Amaya from saboteurs and infiltrators," said Balafam.
"I'm fully confident because most of the Iraqi Coastal Defense Force personnel are from the former Iraqi navy and I'm confident about their skills."