The agency started probe on the instructions of the high court which had handed over the case to CBI and criticised the state police for their shoddy investigations in the murder in which BJP MP from Junagadh Dinu Bogha Solanki's nephew Shiva Solanki was arrested for allegedly carrying out the killing but the MP was given a clean chit.
The agency has registered the FIR against unknown persons under Section 302 (murder) of IPC, CBI sources said.
The team of special crime unit would soon be reaching Ahmedabad to initiate its probe in the case, they said.
A Right to Information (RTI) and environment activist, Gujarat-based Jethwa, who had filed numerous RTI applications and a PIL against illegal mining in Gir forest region, was shot dead outside the Gujarat High Court on July 20, 2010.
The killing had sparked an uproar among the RTI activists across the country who raised concerns over the safety of such whistleblowers.
His father Bhikabhai Jethwa had sought a CBI probe alleging that Dinu Bogha Solanki was behind the murder.
In his plea before the high court, Bhikabhai has alleged that state police had not properly probed the case and the state government was shielding the BJP MP.
The division bench of Justices D H Vaghela and J C Upadhyay, on September 25, while handing over the case to CBI had observed that investigation in Jethwa murder case was "far from fair, independent, bona fide or prompt".
The high court had also rapped the state police for its shoddy probe.
"It has come on record that Shiva Solanki (nephew of BJP MP and prime accused in the case) and DB (Dinu Bogha Solanki) were living together in a joint family and no investigator could have been easily satisfied with the statements that they did not interact in respect of the conspiracy to commit a capital crime," it had said.
Police had arrested six persons including Shiva and sharp shooter Sailesh Pandya, who had shot at Jethwa but it ruled out any involvement of Dinu Bogha Solanki in the murder.
The court later directed the police to specifically probe the role of the BJP MP but Solanki got a clean chit again.
Jethwa had filed several petitions in the Gujarat high court including a Public Interest Litigation in connection with illegal mining in Gir forests in Junagadh district which is a protected area and last home to Asiatic lions.
The bench while conceding the demand of the RTI activist's father Bhikhabhai, had severely criticised the investigation into the case conducted by Gujarat police.
"The commission of murder, in the facts of the present case, amounted to an affront to the judicial system and a challenge to implementation of an Act of Parliament, with national repercussions and has to be viewed seriously," the bench had observed.
It had asked the central agency to complete further investigation and file the report, preferably within six months.
"Murder of a petitioner in a PIL and an RTI activist, in front of the high court, could be read as a clear message to the concerned citizens that they may have to pay by their lives, if they insist upon using the tools placed in their hands by law and approach the court for redressal of public rievance against some individuals," it had said.