Fallujah, a city in the Iraqi province of Al Anbar, has been held by al-Qaeda-linked militants for weeks.
"Military operations taken against selected terrorist organization targets in Fallujah have been stopped for 72 hours," the ministry said in a Saturday statement.
The decision was made "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.
The announcement raises the possibility of a negotiated end to the crisis.
On Saturday, Iraqi security forces succeeded in regaining full control of a northern town of Sulaiman Bek, flushing the al-Qaeda-linked militants out of the area.
The takeovers in Anbar province are the first time al-Qaeda-linked militants have exercised such open control in major cities since the bloody insurgency that followed the US-led invasion of 2003.
More than 370,000 people may have been displaced by Anbar violence, according to the UN.
RA/MB