The RSS activist was murdered in October at Bengaluru following which a case was registered by the Commercial Street police station.
During the course of the probe, the police had learnt that the case had an inter-state ramification.
The police had arrested five persons including a senior leader of the Popular Front of India.
The decision to hand over the probe to the NIA came after it had been found that the case had inter-state ramifications.
While the murder was committed by locals from Bengaluru, it is suspected that orders may have come from Kerala.
The Home Minister of Karnataka, Dr. G Parameshwar had told the assembly recently that the accused in this case had links with the Indian Mujahideen, SDPI, PFI and al-Ummah.
He also said that in the past three years nine persons associated with either the BJP or RSS have been murdered.
He said that the suspects in the recent murder case of RSS worker, Rudresh are said to have links with SDPI, PFI, Indian Mujahideen and Al Ummah of Tamil Nadu.
The NIA would probe the conspiracy and also the motive behind the murder.
The BJP has been crying foul and says that the murder was a politically motivated one.