The roadside bomb hit Saadun al-Dulaimi's convoy as it travelled between Fallujah and Ramadi, "wounding two of his guards and damaging one of the vehicles," the ministry said on its website.
It did not specify whether or not Dulaimi was travelling in the convoy, but a senior defence ministry official told AFP that he was not present at the time of the attack.
The bombing comes after five senior officers, among them a divisional commander, and 10 other soldiers were killed on Saturday during an operation against militants in Anbar, the same province in which Dulaimi's convoy was travelling when it was attacked.
"Military operations are continuing in Anbar 24 hours per day, and we are focusing on areas near the border," the senior official said, adding there was a major deployment along the Syrian border to stop the movement of militants and weapons.
Yesterday, defence ministry spokesman Mohammed al-Askari said Iraqi forces had destroyed two militant camps in Anbar.
Such camps have proliferated in areas near the border with neighbouring Syria, where a brutal civil war has bolstered militant groups and fuelled violence in Iraq, Askari said at the weekend.
This has encouraged Al-Qaeda-linked militants to "revive some of their camps that were eliminated by security forces in 2008 and 2009," Askari said, adding that aerial photos showed 11 militant camps near the border with Syria.
"Photographs and intelligence information indicate that whenever there is pressure on armed groups in Syria, they withdraw to Iraq... To regroup and then carry out terrorist operations in the two countries," Askari said.
More than 6,650 people have been killed in Iraq since the beginning of the year, according to AFP figures based on security and medical sources.