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The agency has arrested Dinesh, Sunil, Nutan, Ashwath, Shahnawaz and Nazeer Ahmed in an operation which is still on, they said.
These are the first arrests in the case which was taken over by the Central Bureau of Investigation (CBI) in September last.
The accused were produced before a special court in Bengaluru which sent them to five days of CBI custody, they said.
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The CBI, however, did not offer any official comment on the role of the accused as their questioning is still going on.
Gowda, the BJP taluka panchayat member, was killed in his gym on June 15, 2016 by unidentified men.
The agency took over the probe on the recommendation of the Karnataka government on September 24, 2019, they said.
Gowda ran a gym at Sapthapura in Dharwad and was a friend of Basavaraj Shivappa Muttagi, the prime accused, for the last 10 years with different political inclinations.
Gowda came to know about a land purchase deal by Muttagi. Gowda had threatened Muttagi that he should not purchase the land as it was under the former”s custody and if he still proceeded, he would kill him.
The Karnataka 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 was handed over to the CBI.