He claimed Prime Minister Narendra Modi and Bhide had good relations.
"Maharashtra Chief Minister Devendra Fadnavis had assured on the arrest since an FIR had been registered. But when we inquired, we learnt the message had come from the Prime Minister's Office not to arrest Bhide or take action against him," Mr Ambedkar told the media here.
"PM Modi had worn saffron turban during his first speech from the Red Fort on Bhide's advice. PM Modi praised him in an event. This is the relation."
He warned that in case there is no response from the government, his organisation will take the issue across the country.
The Dalit leader said Bhide had not even filed any application for interim bail since he was quite sure that the PMO was protecting him.
Prakash Ambedkar, grandson of the Indian Constitution's chief architect Dr BR Ambedkar, demanded that Bhide and another pro-Hindutva leader Milind Ekbote be arrested immediately for the Bhima-Koregaon violence.
"Unscrutinised and loose" organisations in the Hindu fold had become a threat to society and the nation, said Prakash Ambedkar, chief of the Bharipa Bahujan Mahasangh.
"These unscrutinised organisations are dictating terms and so the government is hesitant to take action against them," Mr Ambedkar said.
"They are declaring themselves above the law. That is what Hafiz Saeed is doing in Pakistan: He has positioned himself in such a way that the Pakistan government cannot touch him even when international forces are asking for action. We will not like to have another Hafiz Saeed in India," he said.
"The RSS had stated that relations with Bhide were severed seven years ago and with Ekbote some eight years ago," he said.
Clashes broke out on January 1 in Bhima-Koregaon and surrounding areas in Maharashtra during celebrations of the Battle of Bhima-Koregaon, after some people carrying saffron flags pelted stones at cars going towards the village.
The violence spread to Mumbai and other parts of the state on January 2 and January 3, with protesters calling for a bandh across Maharashtra.