A bench headed by Justice Aftab Alam dismissed the petition when it was mentioned for urgent hearing.
Former Kerala chief minister K Karunakaran and former Chief Vigilance Commissioner (CVC) P J Thomas were also accused in the case.
The proceedings abated against Karunakaran following his death and Mr Thomas who is facing trial in the case, was removed from his post by the apex court.
According to the petitioner, Mr Chandy was also a Minister in the Karunakaran government when the fraud took place in 1999.
A total loss of Rs 2.08 crore was caused to the state exchequer in the scam involving the import of palmolein.