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Gowda, a BJP Zilla panchayat member, was killed in his gym on June 15, 2016, by unidentified men, they said.
The agency has taken over the probe on the recommendation of the Karnataka government, they said.
It is alleged that Gowda was running a gym at Sapthapura in Dharwad. He was friends with Basavaraj Shivappa Muttagi, the prime accused, for the last 10 years with different political inclinations.
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Gowda had threatened Muttagi that he should not purchase the land as it was in his custody and if he still proceeded, he would kill him.
The state police had already completed the probe and filed a charge sheet against six accused on September 9, 2016.
It is alleged that Muttagi hatched a criminal conspiracy to kill Gowda.
When Gowda came to his gym on June 15, 2016, accomplices of Muttagi sprinkled chilli powder on his face and hacked him to death.
The killers escaped on three two-wheelers. The case is under trial in the District and Sessions Court, Dharwad.
After the change in the Karnataka government, the matter has been handed over to the Central Bureau of Investigation (CBI).