The ministry gave no details of where or when Karuna was arrested or what would happen to him.
A Tiger offensive recaptured his territory and he was said to have fled to government controlled parts of Sri Lanka.
His group now controls large sections of the east of the country and has been accused of abductions, killings and other human rights abuses.
Diplomats and analysts say Colombo was using Karuna as part of its fight against the Liberation Tigers of Tamil Eelam (LTTE) or Tamil Tigers, who aim to carve out an independent homeland for the island's Tamil minority.
Sri Lanka's government denies backing Karuna's fighters.
A 2002 ceasefire collapsed last year, with the island now back in a two decade long conflict that has already killed about 70,000 people.