Special Task Force (STF) commandos found the chambers at a rebel camp in the eastern district of Ampara during a nine-day offensive, which ended at the weekend after capturing 12 rebel bases, the ministry said.
"At the Madurakavi camp, torture chambers and lockups were established to torture escapees and informants, including women cadres," the ministry said.
It did not make any claims about what types of torture were employed.
There was no immediate reaction from the rebel Liberation Tigers of Tamil Eelam (LTTE) group to the military's claims.
A Human Rights Watch report released this month accused the rebels and the government of routine extra-judicial killings and abductions in the island's bitter ethnic war, which has claimed more than 60,000 lives since 1972.
The two sides have escalated the conflict in recent months, despite a ceasefire agreed in 2002 but now seen as moribund.
More than 3,800 people have been killed in the fighting since December 2005.
The military, wh