The agency's senior editors denied an earlier state television report that the three men had been kidnapped.
"Local police have arrested three of our colleagues in Iraq," Hassan Lavasani, the head of foreign news at IRNA, said.
He said the bureau chief and two other Iranian reporters had been seized on Wednesday.
But Iran's embassy in Baghdad said two of the men were Iraqi local staff. IRNA's own reports said three local staff had been arrested by the police, along with the bureau chief.
IRNA reports added the agency lost contact with its Baghdad bureau on Monday afternoon.
A former IRNA Baghdad bureau chief, speaking to state
television, said a group of armed men had stormed the IRNA
bureau in Baghdad.
"Neighbours said they were police and we have sent an
inquiry through the embassy to clarify whether they were and
where they have been taken to," he said.
Journalists from Iran's state television said they had made
unsuccessful inquiries to the Iraqi police on the whereabouts of the men.
Wednesday's arrests mark the latest in a series of incidents involving the detention of Iranian journalists in Iraq. On 1 July 2003, two Iranian TV journalists were detained by US occupation forces for alleged "security violations" in Kut.
Saeed Abutaleb and Soheil Karimi of Iran's Channel 2 were placed in a high-security detention facility near Baghdad airport. Iranian officials said the two men and their local support staff had been filming a documentary on Shia in Iraq's south.
The two men were released after four months. They alleged severe torture and humiliating containment conditions while detained.
US occupation forces at the time denied they tortured anyone in their detention facilities.