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Mr Ganapathy, a Deputy Superintendent of Police, was found hanging in a lodge around 270 km from Bengaluru last July.
In an interview, the 51-year-old officer had accused Mr George - then home minister - and two police officers of harassing him and said they should be held responsible "if anything happens to me".
Mr Ganapathy was being investigated for charges of corruption and fake encounters or extra-judicial killings.
Mr George resigned days after the suicide when a court, responding to a request from the police officer's son, asked for a police case.
He returned to the government after the state Criminal Investigation Department or CID told the court it had found no evidence linking Mr George with the death.
The Supreme Court then ordered a CBI investigation saying that "startling facts" in the case needed to be probed.
"This is political. Let the CBI investigate, they've taken the older case into account rather than what Supreme Court ended with in its judgement," Mr George, Karnataka's Bengaluru City Development Minister, said.
Chief Minister Siddaramaiah, backing his minister, accused the central government of pushing the CBI to target his colleague just months before state elections." This attitude of BJP is to make political gain and since Elections is fast approaching they are making it political issue," he said.
The Chief Minister is facing renewed BJP allegations that he had deliberately tried to prevent an independent probe by the CBI into the death.
Karnataka goes to polls early next year. The CBI case against a minister adds to the list of flashpoints between the Congress and the BJP. Earlier this week an old controversy surrounding 18th century Mysore ruler Tipu Sultan resurfaced.
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