Bhatkal is wanted in several bomb blast cases.
"Bhatkal, along with Akhtar, was arrested by a team of Bihar Police and NIA personnel from Raxaul, on this side of the Indo-Nepal border,” said additional director general (headquarters) Ravindra Kumar. "We had inputs from various intelligence agencies, and on the basis of these inputs, the Motihari superintendent of police made the arrests."
According to senior police officers, Bhatkal and Akhtar would soon be flown to Delhi for further interrogation by NIA.
According to sources, the Intelligence Bureau tracked their movements for at least a month.
The two suspects were arrested late on Wednesday evening and brought to Bettiah in West Champaran district around midnight.
Bhatkal was moved to Motihari on Thursday morning, where he was produced before a court for transit remand.
Kumar confirmed the state police had handed them over to NIA. The agency is, reportedly, sending a special aircraft on Friday morning to bring them to Delhi.
The agency is also said to have decided to conduct a DNA test to confirm Bhatkal’s identity.
One of India's most wanted men, Bhatkal is accused of terror strikes in Delhi, Mumbai, Bangalore, Pune and Hyderabad.
The 30-year-old allegedly co-founded Indian Mujahideen with his brother Riyaz Bhatkal and Abdul Subhan Qureshi.
Security agencies in the country had been looking for him for five years.