The announcement raises the possibility of a negotiated end to the crisis, during which gunmen also seized parts of Anbar provincial capital Ramadi, west of Fallujah.
"Military operations taken against selected terrorist organisation targets in Fallujah have been stopped for 72 hours," the ministry said in a statement of the city just a short drive from Baghdad.
The decision was taken "in response to goodwill and frequent communications with forces of good and people calling for peace, and to stop the bloodshed in Fallujah," it added.
More than 370,000 people may have been displaced by Anbar violence, according to the UN.
Violence in Iraq has reached a level not seen since 2008, when the country was just emerging from a period of brutal sectarian killings.
Violence has killed more than 580 people so far this month and upwards of 1,550 since January 1, according to AFP figures based on security and medical sources.