"Merely having photos with the prime minister or Maharashtra chief minister doesn't mean that they (Bhide and another Hindutva leader Milind Ekbote) are protected. I disagree," Athawale told reporters when asked to comment on Ambedkar's claim.
He said the NDA government would never shield any accused persons and would take a stern action against such elements.
Ambedkar, president of the Bharip Bahujan Mahasangh, had said in Delhi that Bhide was being shielded by the PMO.
Addressing a press conference here, Athawale said he was hopeful that Ekbote and Bhide would be arrested soon.
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One man was killed when clashes broke out between Marathas and Dalits on January 1, 2018 during an event to mark the bicentennial anniverary of the Koregaon Bhima battle.
Ekbote, Bhide, and others were booked under the SC/ST Prevention of Atrocities Act, Arms Act, and for attempt to murder and rioting of the IPC.
Athawale demanded a stringent action against "perpetrators" responsible for the caste violence.
He said several complaints, facts and reports indicate the alleged involvement of Bhide and Ekbote in the violence.
"I have spoken to the police and was briefed that there is a collecting evidence to make a strong case against both the leaders," Athawale said.
The minister said the social fabric of the state will get disturbed if Marathas and Dalits keep fighting with each other.
"The disturbed social fabric will hamper the economic development of the state," he said.
"B R Ambedkar's ideology cannot go hand in hand with the Naxal ideology," the RPI(A) president said.
Alleging that the Koregaon Bhima violence was "premeditated", Athawale said the police had failed to gather intelligence about the brewing trouble.
However, the minister praised the police for their handling the situation in the aftermath of the clashes.
"The situation had arisen in neighbouring Vadhu village but it was defused subsequently with the intervention of the police," he said while referring to the incident ahead of the caste clashes.
"On that particular day, a mob of around 1500 people gathered and violence broke out," he said.
He said Naxals had no role in the Koregaon Bhima violence.
Athawale also took a dig at the opposition for organising a rally on January 26 in Mumbai to save the Constitution.
"Narendra Modi government is committed to safeguarding the Constitution in letter and spirit. The opposition should not worry about the Constitution as the government is committed to strengthening it. I and Modiji are there to safeguard it and the opposition should not worry about the same," he said.
In dalit narrative, the battle is viewed as the defeat of "casteism" of Peshwas as the British forces comprised many dalit soldiers.