They surrendered at the Indian border post of Dawki, in northeastern Meghalaya state, just steps away from Bangladesh.
Rajkhowa has long been believed to operate from Bangladesh.
The militants were "roaming about on the Indian side when our troopers came in contact with them leading to their surrender," Gandhi said by telephone.
ULFA has fought for an independent homeland for ethnic Assamese people in India´s northeast for the past two decades. At least 10,000 people, most civilians, have died in Assam state because of fighting between government forces and ULFA rebels, as well as with another separatist group, the National Democratic Front of Boroland.
ULFA has suffered a string of setbacks over the past year, with several top commanders arrested. After Friday´s surrender, the only top ULFA leader at large is military commander Paresh Baruah.
Officials said he may end his fugitive days soon.
"We have information that Paresh Baruah is currently based on the China-Myanmar border and hope he will accept our standing offer of peace talks," Assam Chief Minister Tarun Gogoi said.
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