The violence-torn country topped the organisation's annual survey of journalists' killings, which totalled 100 worldwide last year, making it the worst year since IPI started recording them in 1997, Vienna-based IPI said in a statement.
"Journalists and media workers have emerged as a clear target for insurgent attacks," IPI said in the survey.
"Media representatives have been repeatedly victimised by sectarian death squads intent on silencing outspoken voices through violence and intimidation," it added.
Of the 46 journalists killed, 44 were Iraqi nationals, several of them working for international media outlets, it said.
The total was largest of any year since U.S.-led troops toppled Saddam Hussein in 2003.
The organisation, which was founded in the United States in 1950 and has members in 120 countries, blamed the Iraqi government for not prosecuting journalists' killings and for tightening its own grip on the media at the same time.
"Journalists have faced threats, criminal prosecution and imprisonment and news organisations have been banned over coverage that displeases the authorities," IPI said.
"The Iraqi government's policies towards the press closely resemble those of autocratic regimes in the region, and not those of an aspiring democracy."
Ten journalists were killed in the Philippines and seven in Mexico, IPI said.