CBI sources said residence of Akolkar in Pune and that of Hindu Janajagruti Samiti member Virendrasing Tawde in Panvel near Mumbai, were searched by the agency today.
They said the two came under scanner after the agency found some "cyber forensic evidence" about their alleged role in the murder case of Dabholkar.
They said during the investigation in the Dabholkar murder case, continuing for last two years, the agency had found some emails which were being analysed. It was during the forensic analysis of these emails, that the CBI found material which indicated that these could have could be linked to the murder case.
34-year-old Akolkar is suspected to be one of the key conspirators in the murder of Dabholkar, a rationalist who fought against superstitions all his life, on August 20, 2013 in Pune.
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Akolkar is believed to be linked to 'Sanatan Sanstha', a Hindu right wing organisation whose headquarters are located in Ponda, Goa.
He has been on the run ever since his name cropped up during NIA investigations in the Goa blast case.
Two alleged Sanatan Sanstha operatives were killed when the bomb they were carrying accidentally exploded on Diwali eve in Margao in Goa. Six other accused, who had been charged with waging war against the nation in the case, were later acquitted by an NIA court.
The blast had occurred at a place not far from where the then Goa Chief Minister Digambar Kamat was attending a function.
The NIA charge sheet was dismissed on technical grounds by a special court in December 2013 as the agency had not sought sanction of the state government against the accused who were also charged under Explosive Substances Act. NIA has filed an appeal which is pending before Goa bench of Bombay High Court.