The crackdown will take about two weeks "and then law will be imposed in all Diyala," Bajilan said by telephone, providing new details about the operation that began Tuesday.
The Iraqi Defense Ministry spokesman, Maj. Gen. Mohammed al-Askari, said that 35 "wanted insurgents" have been apprehended so far and a number of weapons seized.
Diyala has been one of the hardest provinces to control despite numerous military operations. Baquoba has enjoyed security improvements recently but continues to see attacks, such as twin suicide bombings that killed at least 28 people on July 15 and a number of suicide attacks carried out by female bombers.
"We are not fighting an organized army but we are fighting terrorist groups hiding either in palm tree orchards or among civilians," al-Askari said, adding that the rugged nature of the big province further complicates the anti-insurgent effort.
The operations were primarily carried out by Iraqi security forces in the latest display of Iraq's readiness to take over its own security and enable American troops to eventually withdraw.
The U.S. military was providing intelligence, fire support and logistics as Iraqi forces gradually assumed front-line roles, a factor that contributed to sharp decrease in the number of U.S. troop deaths this year.
U.S. military spokesman Brig. Gen. David Perkins said the main challenges in Diyala were the hot summer temperatures and the abundance of hiding places in palm groves and other agricultural areas.
"It just takes a lot of physical effort to go through this difficult terrain and very hot and demanding conditions," Perkins told a joint news conference with al-Askari.
Perkins also said U.S. and Iraqi forces had coordinated their efforts in the run-up to the operation to minimize collateral damage and the impact on civilians.
"The cooperation that we are getting from the people who live in Diyala is exceptional," Perkins said.
Sunnis in Diyala and elsewhere often have complained of discrimination at the hands of the Shiite-led government, saying it was focusing on security in Shiite areas.
Diyala, a religiously mixed province that controls key supply routes to Baghdad and northern cities, also has been the scene of kidnappings and sectarian killings between Shiites and Sunnis.
A triple suicide bombing that left 32 people dead during a Shiite procession on Monday in Baghdad was also blamed on sectarian violence. Another suicide attack in northern city of Kirkuk killed 25 people the same day. The U.S. military blamed al-Qaida in Iraq for both attacks.
But an al-Qaida front group in Iraq denied responsibility posted an Internet statement denying responsibility for the bombing of Shiite Muslim pilgrims.
"Any act that we don't claim responsibility for, is not ours at all," the group said.
Instead, the Islamic State of Iraq says it's starting a campaign of attacks in the northern city of Mosul "in revenge for the blood of our hero brother." It's referring to one of its militants, but didn't say when he was killed there.
U.S. and Iraqi forces have been battling al-Qaida-inspired insurgents in Mosul for months.
In violence Wednesday, a roadside bomb targeted an Iraqi army patrol in eastern Baghdad, killing at least one Iraqi soldier and wounding seven other people, police said.