Sharad Kalaskar was one of the two shooters who allegedly killed anti-superstition activist Narendra Dabholkar in August, 2013, the Central Bureau of Investigation told a Pune court on Tuesday.
The court remanded him in the central probe agency's custody till September 10.
The other alleged shooter, Sachin Andure, is now in judicial remand.
Kalaskar is an expert in 'weapon handling' and was involved in 'making of bombs', the CBI told Judicial Magistrate (First Class) S M A Sayyad.
"During the investigation, it was revealed that Kalaskar was the other shooter, who fired two bullets at Dabholkar along with Andure (who allegedly fired one round)," said CBI lawyer Vijaykumar Dhakne.
The agency wanted his custody to probe his role in the conspiracy further, Dhakne said.
The conspiracy was hatched by Virendra Sinh Tawde (already arrested), Kalaskar and others, he said.
Defence lawyer Dharmaraj Chandili opposed the demand for CBI custody of Kalaskar.
According to the CBI's chargesheet against Tawde, two men, named 'Sarang Akolkar' and 'Vinay Pawar', were the shooters who killed Dabholkar, but now the agency has changed its tune, he said.
The CBI has not yet recovered the firearms and the two-wheeler used in the crime, the defence lawyer pointed out.
Kalaskar was arrested last month by the Maharashtra Anti-Terrorism Squad (ATS) in connection with an alleged conspiracy to carry out blasts in the state.
The ATS had claimed that during interrogation, Kalaskar revealed that he and Sachin Andure were involved in the Dabholkar murder, following which it tipped off the CBI which arrested Andure.
The CBI took Kalaskar's custody from the ATS on Monday.
The agency has also claimed that two men arrested in the journalist Gauri Lankesh murder case by Karnataka police were also involved in the Dabholkar murder conspiracy.
The CBI arrested the two -- Rajesh Bangera and Amit Digvekar -- in the Dabholkar case last week.
While Dabholkar was killed in Pune on August 20, 2013, Lankesh was shot dead in Bengaluru on September 5, 2017.