The shocking incident took place on Sunday, Aug 9 night.
In her statement, the victim said that some army jawans and police officials came to her home at around 10 pm, and started questioning about her husband.
He was not present at home, at that time, so the police officials and army jawans left from her house.
Her husband is reportedly having connection with armed-separatist outfit National Democratic Front of Bodoland NDFB(S).
At midnight, around 2 am, two army soldiers again returned to her house and took her to a nearby school.
Both of them allegedly gangraped her there.
On the basis of her complaint, police registered a case under section 376(2)e/g against the Army personnel of the Moinguri-based camp.
Meanwhile, the Assam government has announced a magisterial inquiry into the issue.
Army denies charges
Army has filed a counter FIR against the rebel group for trying to "malign its image".
A defence spokesperson said the "complaint of alleged rape, is totally false, fabricated, baseless and is an attempt to malign the image of the Army".
A counter FIR has also been lodged by the Army at Kachugaon Police Station against this "effort by the NDFB(S) to malign the Army's image by any possible means".
Based on specific intelligence about presence of NDFB(S) overground workers, a joint team of the army and police launched a joint operation in Karigaon and Thaisaguri villages of the district on Sunday but the operation was later called off as those being looked for were not found.
The defence spokesman also said that no subsequent operation was launched by the army and no security personnel went to the worker's house or his village thereafter.
Initial medical examination of the worker's wife conducted at R N Brahma Civil Hospital in Kokrajhar also did not find any injury mark, no mark of violence and absence of spermatozoa, the spokesman claimed.
Therefore, the complaint of alleged rape, is "totally false, fabricated, baseless and is an attempt to malign the image of the Army. It has been made with the aim to disrupt the momentum of operations and divert the attention of security forces from security operations".
"Few people with vested interest have tried to politicise the issue", the spokesman added.
Earlier in the day, the issue was raised in the Assembly by Bodoland Peoples Front MLA Pramila Rani Brahma.
In his reply, Parliamentary Affairs Minister Rockybul Hussain said the government has ordered Kokrajhar Deputy Commissioner to conduct a magisterial enquiry into the incident.
"We have asked to submit the report within seven days. We will do everything possible to help the victim. Strict action will follow to punish the culprit," he said.
The minister added that the woman was taken for a medical check-up to Rupnath Brahma Civil Hospital and the report was awaited.
(With PTI inputs)