Al Qaeda affiliates are still blamed for much of the violence in Iraq with the insurgency seeking to destabilise the country.
"It was an ambush during which they were captured after we acted on detailed information. We were following them," said Mohammed al-Askari, the defence ministry spokesman.
The four men included Mikhlif Mohammed Hussein al-Azzawi, known as Abu Radhwan, suspected of leading the local group's military operations, and Qassim Mohammed Taher, accused of orchestrating a March attack on a provincial building that killed more than 50 people.
They were arrested in the city of Samarra, 100 km (62 miles) north of Baghdad, Askari said.
Iraqi officials say al Qaeda has been severely weakened, and its two top commanders were killed in April last year. But dozens of bombings, assassinations and attacks are still carried out each month.
Iraqi security officials have been on high alert for revenge attacks by local al Qaeda fighters since U.S. troops killed Osama bin Laden in Pakistan earlier this month.
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