Guns, ammunition and gunpowder were found at the camps in the Mayu Mountains, part of a remote strip of land on the northwest border that is mainly home to the persecuted Rohingya Muslim minority.
More than 70,000 Rohingya have fled the area to nearby Bangladesh since October, when Myanmar security forces launched a brutal crackdown in response to militant attacks on police posts.
Rohingya escapees have told harrowing accounts of security officers slaughtering babies, burning people alive and staging gang rapes -- abuses UN investigators said may amount to crimes against humanity.
The government has refused to allow in a UN fact-finding mission to investigate.
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The training camps found this week were allegedly run by the same group that carried out the October raids that killed nine policemen, according to state media.
The report said security forces killed three "armed attackers in self-defence" during the two day clearance operation, which was launched after they received a tip off the militants were training inside a secret tunnel at night.
The militants, now called the Arakan Rohingya Salvation Army (ARSA), were subsidized by "foreign monetary aids" and spent months training recruits in martial arts and the use of light weapons, according to the government report.
The ARSA has denied killing any civilians, saying it is fighting for the political rights of the oppressed Rohingya.
The one million strong minority live mostly in Myanmar's western Rakhine State, where they are denied citizenship, access to basic services and live in apartheid-like conditions -- many in squalid displacement camps.
Nobel laureate Aung San Suu Kyi, whose civilian government ended decades of military rule last year, has faced global criticism for not defending the Rohingya -- who are maligned by the Buddhist majority -- or condemning the army's brutal crackdown.