According to sources, Apurba Baruah, the outfit's publicity secretary, has also been arrested. Both are expected to be handed over to India soon
The arrests come ahead of Bangladesh Prime Minister Sheikh Hasina's visit to India from Dec 19.
56-year-old, Rajkhowa was in Bangladesh for close to two decades, operating out of bases in that country and ordering hit-and-run strikes in Assam.
He founded the ULFA in 1979 along with five other leaders, including the outfit's commander-in-chief Paresh Baruah, who is believed to have escaped Bangladesh and is reportedly hiding in China.