The top court issued notices to the Maharashtra government and the complainants.
The apex court noted strong observations made by the High Court establishing the necessity for lodging a case against Munde, but failed to see any merit.
"If we allow this, then every other person will go to the High Court for registration of FIR..", said the top court.
Munde's lawyer, senior advocate Amrendran Sharan insisted that the FIR must go, contending that it signifies wrong exercise of jurisdiction by the High Court.
The apex court upheld Munde's lawyer's argument that prima facie no offence is made out against him.
Munde on Thursday had moved the top court challenging the Bombay High Court order. The Vacation Bench, comprising Justices Indira Banerjee and Ajay Rastogi, agreed to hear the matter.
Earlier, the Bombay High Court had directed the police to lodge a case against Munde in an alleged illegal purchase of government land in Beed district.
The court's direction came on a petition filed by Rajabhau Phad, who alleged that the land at Pus village in Ambajogai tehsil, belonged to the government, and it was wrongfully handed over to Belkhandi Math as a gift.
The land transfer took place when Ranit Wyanka Giri was its mahant, despite the fact that the land cannot be transferred without government's permission, Phad contended.
After Giri's death, his family members transferred the land in their names and claimed ownership, and this information was allegedly not shared with the government, the petitioner said.
Later, Munde bought the land in 2012 on the basis of a general power of attorney, according to the petitioner.
Phad also alleged that Munde applied for non-agricultural status (NA) of the land.
He said the police failed to register a case against Munde and that's why he moved to the High Court stating that the government land cannot be sold to anyone.
The petitioner has sought the registration of an FIR under section of forgery and cheating against Munde, his wife and 15 others.