Security officials said the clash occurred Thursday in Assam's Goalpara district after a team of police and army, following a lead, searched Bokapara near Lakhipur along the Assam-Meghalaya border.
"Based on our intelligence input, we had launched the operation at the bordering area," a police official, speaking not for attribution told India Blooms News Service. "When troops reached the area, the hiding militant group started firing and bullets were exchanged."
The GNLA and factions of the militant United Liberation Front of Asom organization established several camps along the border in an apparent attempt to disrupt Saturday's elections in Meghalaya.
In response, Meghalaya and Assam police tightened security in the border region and the area around the Assam Secretariat and other offices have been declared protected areas by the Kamrup (Metro) district authorities.
The order issued by Kamrup Deputy Commissioner Ashutosh Agnihotri says only legitimate residents and public officials of the secretariat and other offices can enter the area without prior permission.
Former Meghalaya Deputy Superintendent of Police Pakchara R. Sangma, who uses the alias "Champion R. Sangma," formed the GNLA after deserting the police force. The GNLA has a stated objective of establishing a "sovereign Garoland" in western Meghalaya through armed struggle.
Sangma is GNLA chairman, while former Achik National Volunteers Council area commander for the East Garo Hills Sohan D. Shira serves as GNLA commander in chief. The majority of the GNLA personnel are deserters from the ANVC, the Liberation of Achik Elite Force and National Democratic Front of Bodoland.
The GNLA's primary base of operations is in three GaroHills districts in western Meghalaya state in northeastern India. While the GNLA's initially operated in the eastern and southern Garo Hills, it has started to expand its activities in the coal-rich border regions of the western Khasi Hills, adjacent to the southern Garo Hills.
More worrying to Indian intelligence officials, Sangma has visited Bangladesh to seek support and explore the possibility of setting up a base in Dhaka. A further concern for Indian security officials is that the GNLA has developed links with other militant organizations in northeastern India, including the United Liberation Front of Asom, the NDFB and the National Socialist Council of Nagaland-Isak-Muivah.
Indian intelligence also says the GNLA has initiated a tactical alliance with Bangladesh's A'chik Special Dragon Party militant group, which operates along the Indian-Bangladeshi border in the western part of Meghalaya state.
Both the GNLA and ANVC are listed as terrorist organizations by the Indian government.
Police said many polling stations in the five districts of Garo in western Meghalaya has been classified as "hyper-sensitive" and 10 companies of paramilitary forces have been deployed in eastern Garo Hills to ensure that the regional elections proceed with incident.