"We can only advise (them) but, if in the end, MIC leaders feel the (agreed) proposal will not solve the crisis and they want to do it their way, go ahead," Barisan Nasional party deputy chairman Muhyiddin Yassin said.
"Do what you want to do but if later the party splits and has issues and disputes, don't blame us (the Barisan leadership)," he said.
Malaysian Indian Congress is one of the key components of the Barisan coalition representing the country's minority ethnic Indian community.
He said MIC president G Palanivel had agreed at a meeting with the prime minister, deputy prime minister, his deputy Dr S Subramaniam and Dr Ahmad Zahid to hold a re-election at all levels "but now he's changed his mind again."
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"He should quit doing that and settle this politically instead of filing for a review against RoS (Registrar of Societies) order," Zahid said.
"Be fair to your followers and the Indian community. Let the party be led by those who are qualified and chosen by the party members. How are you going to solve issues pertaining to the Indian community if you can't even solve your party's issues?" the home minister asked.
"We are capable of handling ourselves, and he has no right to question the president's capabilities in solving the Indian community's problems, of which he has no clue whatsoever," Balakrishnan said in a statement.
Zahid was commenting on the application filed two days ago by MIC strategic director A K Ramalingam for a judicial review of the RoS decision to declare the MIC 2013 elections null and void, order it to hold fresh elections or risk facing deregistration.
On re-elections, Balakrishnan said it was Palanivel who had proposed fresh elections on February 1 and Zahid had welcomed the decision the next day.
The legal action comes days after the warring factions in the party - led by party president G Palanivel and his deputy Dr S Subramaniam - had agreed to abide by the RoS directives and hold fresh re-elections.