The Home Ministry has written a letter to the state government to hand over the probe to NIA, the officer said.
Andhra Pradesh Police are probing the blasts case and has formed 15 teams to carry out the investigation.
"The NIA had registered a case against Indian Mujahideen in September last year on its larger conspiracy," the NIA official said.
"In connection with the (February 21) blasts case we have got custody of Syed Maqbool and Imran Khan, who have been brought to Hyderabad today from Tihar jail in Delhi. We are questioning them. The investigation is going on. We have some leads. However, at this point of time, we cannot reveal the investigation details," the NIA officer said.
A court in Delhi had yesterday granted the NIA five-day custody of Syed Maqbool and Imran Khan for their interrogation following which the two were brought to the city by the agency.
The blasts in Hyderabad, which claimed 16 lives, were triggered by powerful IEDs planted near Konark and Venkatadiri theatres in Dilsukhnagar.