He said casualty figures were not immediately known but the training camp, in the Weli Oya region, also contained prison cells and a cemetery with 67 guerrilla graves.
Meanwhile troops moves closer to the rebels' political capital of Kilinochchi, 330 kilometres (200 miles) north of Colombo, with the ministry saying 31 Tigers and nine soldiers were killed in clashes on Saturday.
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The Liberation Tigers of Tamil Eelam (LTTE), who have been fighting for a separate state since 1972, did not comment on the latest fighting.
The figures bring the number of rebels the government has killed since January to 5,912, while 545 soldiers have died in the same period. government death tolls cannot be independently verified. Tens of thousands have died on both sides, in one of Asia's longest running ethnic conflicts.