According to a delayed report, they were held in a joint operation by the Assam Rifles and police on Sunday night near Santila under Haflong police station.
They admitted that they were collecting ransom from businessmen in Haflong, said police.
The three terrorists are identified as Athnath Haflongbar alias Jal (21), Sumit Hojai (21) and Baibendra Kemprai (20).
Security personnel also recovered two grenades, a motorcycle and two mobile handsets from them.