A vacation bench of Justice Arun Mishra said the polling would be subject to the outcome of the matter pendingbefore the Bombay High Court.
The apex court also restrained the outgoing managing committee from taking any financial or important decisions while allowing it to carry out the day to day functioning of the GCA.
The court was hearing GCA's plea against a Bombay High Court order which had constituted a new election committee comprising former judge of Bombay High Court to monitor the election process.
On this, the apex court said, "normally the court would observe the rules and not interfere with an ongoing election process but to maintain the purity and sanctity of the process it has to step in.
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"When there are serious allegations, the court cannot remain a spectator. Let the election process go on," the bench said.
Taking note of charges of "non-transparency", the High Court had yesterday refused to stay the election process and appointed a committee headed by Justice (Retd) A P Lawande and two members, Nitin Sardesai and Rajnikant Lavanis.
It also observed that the decision not to allow some clubs to vote because they did not submit names of their representatives 15 days in advance "appears prime facie to be calculated move on the part of Salkar".
The HC allowed all 104 clubs to vote in the polls on Sunday.
The GCA had allowed only 64 out of total clubs to vote as the rest had failed to submit names of their representatives 15 days in advance as mandated by the cricketing body's constitution.