The defense ministry said on Saturday that the militants were killed in aerial bombardment or artillery fire.
The army has largely been stationed out of Fallujah as militants have taken the control of the city.
Fallujah is in crisis-hit Anbar Province, which is a desert region west of the capital, Baghdad, that shares a border with Syria.
Iraqi forces have been fighting against militants, including those linked to the al-Qaeda group Islamic State of Iraq and the Levant (ISIL), in Anbar.
Violence erupted in the western province on December 30, 2013, when the army removed an anti-government camp in the city of Ramadi.
Iraqi authorities said the camp had been used as “headquarters for the leadership of al-Qaeda.”
Iraqi Prime Minister Nouri al-Maleki has blamed “diabolical” and “treacherous” Arab countries for the recent rise in violence in his country, saying, “Iraq is the target for some countries that are backing terrorism, and backing evil.”
Iraq is now experiencing its worst cycle of violence since 2008.
Also on Saturday, two people were killed in a bomb attack in south Baghdad. Another attack targeting an army patrol north of Baghdad also killed one soldier.
Latest figures released on Friday showed that 1,013 people were killed in bombings and shootings across Iraq in January.
The death toll is the highest since April 2008 when 1,073 people were killed.