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A spokesman said the complex in an abandoned quarry in the restive province of Anbar covered an area the size of four football pitches.
The bunkers are said to contain a large stockpile of weapons and living areas with air conditioning and showers.
Meanwhile, Iraqi authorities said they had arrested an insurgency leader and key al-Qaeda figure in Mosul.
The arms cache was one of 50 found in recent days in Anbar province, west of Baghdad, the spokesman said.
Tips from locals and information from detainees had helped to identify the locations uncovered in the ongoing operation, the spokesman said.