Passersby saw Rampal (52) jumping in the canal and informed the police. His body was fished out about two km downstream, the police said.
His family members claimed that the NIA wanted to make Rampal a witness in the killing of Gupta and and he was fed up with constant questioning by the investigating agency.
On November 30 last year, the Punjab government handed over seven cases, including killing of right wing and religious leaders to the NIA keeping in mind the possible "national and international ramifications" of a conspiracy behind the targeted killings in the state.
Earlier, the state government decided to transfer the killing cases to the NIA as the modus operandi in all of these cases was the same.
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According to officials, it was found that inter-state as well as international perpetrators, handlers, actors and a militancy angle were involved in the criminal conspiracy, to disturb the peace and communal harmony in the border state, by selectively targeting leaders of certain groups.
The Punjab government and the NIA has agreed that the probe needed to be more broad-based as the handlers, conspirators and financers in the targeted killing cases operated from countries such as the UK, Canada and Italy, officials said.
The seven cases handed over to the NIA include the April 2016 Khanna killing of Durga Das Gupta, the president of labour service wing of Shiv Sena, Punjab, the January 2017 killing of Amit Sharma the Zila Pracharak Hindu Takht in Ludhiana, the February 2017 killing of Dera Sacha Sauda followers Satpal Kumar and his son Ramesh Kumar in Khanna and the July 2017 killing of Christian Pastor Sultan Masih in Ludhiana.