Muthalik, who is facing some 45 cases including those relating to promoting enmity between two communities, was welcomed into the party fold in the presence of Karnataka party president Prahalad Joshi, former Chief Minister Jagadish Shettar and former Deputy Chief Minister K S Eshwarappa at a function in Hubli.
But as Congress and other parties latched on the issue to attack BJP and rumblings began within the saffron party, BJP President Rajnath Singh directed Joshi to rescind the move.
Soon after the party chief's call, Joshi said the decision allowing entry of Muthalik has been set aside.
"Due to various reasons, induction of Pramod Muthalik has been set aside under central party direction by the state president Prahlad Joshi," said a statement issued by the party's Karnataka unit.
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Asked about the confusion, Joshi said the decision to induct Muthalik into the party was taken at the state level.
Muthalik, who was arrested after the incident, had apologised for the violence but claimed that their actions were "aimed at protecting the women". The then Karnataka chief minister B S Yeddyurappa had said Sri Ram Sene had "nothing to do" with BJP or the Sangh parivar.
Congress slammed BJP's move to induct Muthalik saying that its leaders, including Sushma Swaraj have been talking about women's empowerment but their party was now "glaringly opposing women's emancipation" and had been exposed.
"You can see this is height of opportunism and I think that women across the country should take a very decisive call on this."
BJP leader and Goa Chief Minister Manohar Parrikar also asked the party leadership to reconsider the decision to induct Muthalik.