The police said that acting on a tip-off, its Special Weapons and Tactics team carried out the raid in a house at Songmegap village which was being used as a hideout for the GNLA militants.
The militants, however, escaped amidst heavy firing from both sides.
Several documents were recovered from the house in which the milistants had taken shelter, the police said.
The GNLA is an outlawed organization in Meghalaya having its stronghold in the three western Garo tribal districts. They were involved in kidnapping and extortion besides killing of security forces and civilians.