Rajkhowa had allegedly led a seven-member ULFA team that underwent training at a location not far from Peshawar along the Af-Pak border in 2005, ET has learnt from people who track insurgent groups in the northeast.
The ISI, which was active in Bangladesh under BNP rule between 2001-05, had arranged fake passports for the seven-member group, of whom two were reportedly from a Tripura-based separatist organisation.
At least four batches of ULFA cadre were trained along the Af-Pak border.
Rajkhowa was also a member of the ULFA batch that had undergone the longest training in Myanmar – for seven months – after he joined the outfit in 1988.
Several rebel groups in the northeast also operated out of bases in Myanmar along the more than 1,600 km border.
The Pakistan Army and ISI had for decades abetted and aided several insurgent groups in the northeast, including ULFA, till Sheikh Hasina returned to power in 2008.
In recent months, ISI has been trying to revive plans to support rebel groups through India’s neighbouring countries.
While the Hasina government in Bangladesh has adopted a zero-tolerance policy towards terrorism, including northeast insurgents, Dhaka-based Pakistan diplomats have allegedly initiated plans to back the rebels including from ULFA, ET had earlier reported.
Rajkhowa has been accused of maintaining contacts with Pakistani diplomats and probably having a meeting with the Pakistani High Commissioner in Dhaka, ET had reported previously.
He is also alleged to have maintained close contacts with the radical Jamaat-E-Islami and the Bangladesh National Party. The combine had sheltered several Indian insurgents from the northeast when they were in power in Dhaka during 2001-06 and 1991-96.
Joint efforts by India and Bangladesh security agencies foiled the Rajkhowa-Pak move, leading to the gunfight and his surrender along the Indo-Bangladesh border.
Bangladesh government sources had told ET that it was worried because Rajkhowa could have targeted the Bibiyana gas fields in its Sylhet region to avenge the crackdown on northeast insurgents by the Hasina government.