A bench comprising Justices S A Bobde and A M Sapre initially questioned the locus of Pawar and later asked him to move the Bombay High Court with the plea.
Senior advocate Amrendra Sharan, appearing for Pawar, said the Bombay High Court had appointed two former judges, Justices Hemant Gokhale and VM Kanade, in the Committee of Administrators (CoA) to run MCA and their term ended on September 15.
The former judges did not agree to the extension of their term and the MCA CEO C S Naik did not have the authority to sign the cheques and this had led to a situation where all the financial activities of the cricket body has come to a standstill, he said.
The employees and the players have not received salaries as the MCA is lacking authority to operate MCA bank accounts.
The bench said that it was not dismissing the concerns and was merely saying that the right forum would be the high court.
Referring to the high court's order by which it had earlier refused to entertain a similar plea, the apex court said that now it was clarifying the earlier order and there was no impediments in the high court dealing with the fresh petition on the issue.
The bench said that the apex court had already decided the petition pertaining to implementation of the Justice R M Lodha panel recommendations to reform BCCI.
It said that now the Constitution of the BCCI is registered and in force, it did not want to deal with the plea of Pawar.
Due to the void in the MCA, the association has been unable to clear their electricity dues, property tax, staff salaries, players expenses and payments to various vendors, the NCP leader argued.