Passing the order, Special Vigilance Judge S Jagadeesh, rejected the report filed by investigators in April last stating there was no need for further probe to add any more person to the list of the accused.
The judge asked the Vigilance and Anti-Corruption Bureau to submit the probe report within three months.
The Chief Minister's spokesman said Chandy would react to the court order after examining it closely.
The long-pending corruption case had cost P J Thomas the post of Chief Vigilance Commissioner. Thomas was listed as the sixth accused in the case relating to import of 32,000 tonnes of palmolein from Malyasia causing loss to the tune of Rs 2.32 crore to the excehquer.
Thomas, whose appointment as CVC was quashed by the Supreme Court, was the food secretary then and a director of the state Civil Supplies Corporation. Late Congress leader Karunakaran was the first accused in the case.
The case had taken a politically significant turn in March this year on the eve of the assembly polls with former Food Minister and Congress leader T H Musthaffa mentioning Chandy''s name in his discharge plea.
Mustaffa, also from the Congress, had pleaded that justice given to Chandy by not making him an accused in the case should be given to him (Mustaffa) also.
Seizing on the development instantly, the previous CPI(M) led-LDF Government filed a petition seeking further investigation in the case stating more persons were likely to become accused.
The Vigilance investigators, however, later filed a report stating there was no evidence to include Chandy or any others in the list of the accused.
Significantly, that report was filed in the court a few days before Chandy was sworn in as chief minister.
The sudden cropping up of his name during the election time had caused deep embarrassment to Chandy, who was the front runner for the chief minister''s post.
He had then taken the position that he would face the case "legally and morally".
Central Congress leaders also threw their weight behind Chandy, discounting the chances of considering any other leader for the post of chief minister.