NIA special judge I.S. Mehta also sent another Indian Mujahideen operative, Asadulla Akhtar alias Haddi, to a similar 12 days NIA custody.
Bhatkal and Haddi were produced in a Delhi court after they were flown from Bihar on transit remand.
Bhatkal, arrested Wednesday night, tops the Delhi Police list of 15 most wanted terrorists involved in bombings across the country.
He is a key suspect in the 2008 serial bombings in Delhi's Connaught Place, Gaffar Market and Greater Kailash areas which claimed 26 lives and injured 133 people.