The Assam government meanwhile announced a magisterial inquiry today into the issue.
An FIR was filed by the woman, who is eight months pregnant, at Kachugaon police station alleging that few Army personnel took her to a school building from her house and two of them raped her during the wee hours yesterday.
On the basis of the complaint, police registered a case under section 376(2)e/g against the Army personnel of the Moinguri-based camp.
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".
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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.
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".
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.