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One National Security Committee soldier was also killed in the operation, and another was seriously wounded and hospitalized, it said.
"The IMU members were spotted and surrounded in Jalal-Abad in the early hours of June 23, following a lengthy search period," it said.
The militants were hiding in a private house in a Jalal-Abad suburb, it said.
"During the special operation, the IMU militants put up fierce resistance, using automatic weapons, hand grenades, and other types of explosive devices," it said.
Preliminary findings indicate that the militants had undergone training at international terrorist centers and entered Kyrgyzstan from abroad, it said.