Security forces found briefing rooms containing detailed maps at the facility in the district of Mullaittivu, where the Liberation Tigers of Tamil Eelam (LTTE) have been penned in after a series of battlefield defeats.
"We have captured the main LTTE command centre in Dharmapuram," army spokesman Udaya Nanayakkara said, adding that troops were conducting clearance operations in the area.
He said soldiers also found a communications room within the complex, but the guerrillas had dismantled the equipment and removed it as troops moved in on Wednesday.
"We think it is a very significant place because they had maps of our brigade-level camps," Nanayakkara said.
"This must have been a key centre they used."
The Tiger rebels have been waging a drawn-out fight for independence for the island's minority Tamils since 1972.
However, they have been steadily losing ground since 2007 and have now been confined to the jungle and lagoon district of Mullaittivu where they are known to h