They also said that the 12 "bases" the military had captured consisted of huts belonging to civilians fleeing recent fighting.
The separatist group invited international organisations to investigate the "torture chamber" allegations and claimed that the commandos had taken a "prison" they had abandoned a year ago.
"They [the cells] are more than six feet tall and the size of a standard prison cell to be found around the world," the Tamil Tigers said in a statement. "These were abandoned by the LTTE more than a year ago when LTTE moved further inland."
The defence ministry did not give details of the type of torture carried out by the Tamil Tigers.
"At the Madurakavi camp, torture chambers and lockups were established to torture escapees and informants, including women cadres," the ministry said.
The police released pictures of the bases they claimed to have captured together with a haul of arms, ammunition, bombs and motorcycles.
A Human Rights Watch report released earlier this month accused both the Tamil Tigers and the government of routine extra-judicial killings and abductions during the bitter civil war, which has claimed more than 60,000 lives since 1972.
A deal between Sri Lanka's ruling party and the opposition which aimed to bring a political solution to the conflict has collapsed.
The Sri Lanka Freedom Party and the right-wing United National Party (UNP) had agreed in October to work together to end the violence but the agreement fell apart after the president ruled out stopping UNP defectors being appointed to the cabinet.
"From the minute the cross-overs are accepted to the cabinet, our memorandum of understanding will cease to exist," Jayalath Jayawardena, the UNP spokesman, told AFP news agency.
Sri Lanka's international backers, including the US, European Union and Japan, had wanted the two main majority Sinhalese parties to build on their October deal to offer a consensus plan to the separatists.