He also noted that the incident took place in an area, where bomb blasts had occurred earlier.
The name of some right-wing extremist organisations had surfaced in the 2010 Pune bomb blast.
Asked whether he was suggesting the hand of any right wing terror group behind it, Singh said, "Let the investigating agency do their job."
"I strongly condemn the killing of Narendra Dabholkar fighting superstition. Police must identify the killers, also the people behind the killing," Singh said on microblogging site Twitter.
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He declined to go into "Whose hand is behind it and whose hand is not" but added "the incident has happened in an area, where bomb blasts have happened."
Political parties and social organisations have called for a bandh in the city today to protest the murder of the anti-superstition crusader.
The 69-year-old social activist was shot dead by two motorcycle-borne unidentified assailants yesterday.