The Bhutanese Army on Wednesday overran six camps, including two of United Liberation Front of Asom, housing over 3000 heavily armed anti-India militants in four districts bordering Assam.
Initial reports indicated that over 90 ultras have been killed and the chief of Kamtapur Liberation Organisation Tom Adhikari arrested.
Meanwhile the ULFA urged the Bhutan government to stop its operations. But the government said it undertook the operation after all attempts at a peaceful solution failed.
"The militants never took any negotiation seriously," a government spokesman said.
The Indian Army, which has sealed the border with Bhutan in Assam and West Bengal, was conducting 'complementary exercises' to prevent any of the fleeing ultras from entering the Indian territory, a Bhutan government statement said.
Around 6,000 troops of Royal Bhutan Army overran the ULFA general headquarters in Merengphu under Samdrup Jongkhar district.
The main National Democratic Front of Bodoland (NDFB) camps in Tikri, Samdrup Jongkhar and Nganglam and the KLO camps in Samtse, besides the ULFA central Headquarters have also been captured since the operations began on Monday.
The pace of the operations is being hampered as the areas leading to the camps situated in strategic heights in rugged jungle terrain are heavily mined and insurgents numbering more than 3,000 were using heavy weapons, Bhutan's Foreign Ministry Director Yeshe Dorji told PTI over phone.
Although both sides have suffered casualties, the total number of deaths and injuries were not known at present, the Bhutanese statement said.
But intelligence sources in Guwahati said 90 militants and 34 Bhutanese soldiers have been killed in the intense fighting underway to evict the separatists from 30 well-fortified camps in Himalayan Kingdom.
Of the insurgents killed, 40 belonged to NDFB, 38 to ULFA and 12 to KLO, intelligence sources said.
The captured camps housed armed women cadres and wives and children of insurgent leaders and senior cadres, the Bhutanese statement said.
The Indian army has been very helpful in airlifting injured Bhutanese soldiers as a result of which they were getting immediate treatment, it said.
ULFA chairman Arobinda Rajkhowa, meanwhile, urged Bhutan King Jigme Singye Wangchuk to call off the operations citing 'historical bonds' between people of the region and the royal kingdom.
Claiming that the army operation was 'totally illegal', Rajkhowa said in a letter: "There shall be no extra-legal presence of the ULFA the next moment of resolution of (its) conflict with New Delhi."
Bhutan is a 'temporary refuge' of the ULFA, he said. But that 'did not tantamount to defying the sovereignty of Bhutan or violation of international law', he added.
He also reminded the Bhutanese government about the talks it allegedly held with him and ULFA commander-in-chief Paresh Baruah without mentioning the content of such discussion.
The Bhutanese government said it was in close touch with India and remained confident that the insurgents would be flushed out from its soil, which they have 'forcefully occupied for over 12 years'.
It regretted that the long and arduous process undertaken by it to find a peaceful solution leading to peaceful departure of the insurgents from the country did not yield any fruit even after six years of negotiations, which were always initiated by the royal government.
"It is particularly regrettable that the militants never took any of the negotiations seriously. While Bhutanese side was always represented by the Home Minister and lastly, even by the Prime Minister, their side was usually represented by mid-level representatives who could not take any decisions," the statement said.
It said when all efforts to find a peaceful solution failed, the government, in the hope of avoiding bloodshed, gave the militants a 48-hour notice through the national newspaper Kuensel.
This too, the statement said, was not heeded to by any group. "It was, therefore, upon havnig exhausted all options and every effort to find a peaceful solution that the current action was taken," it said.