Chandy, accused of land encroachment for his luxury resort, had challenged a report by Alappuzha district collector in this regard.
The minister's resignation came in the wake of a division bench of Justice P N Raveendran and Justice Devan Ramachandran making stinging observations and rapping him for filing a plea against his own government on Tuesday last.
There is a violation of collective cabinet responsibility by the minister, the court had held.
They had abstained from the meeting of the Council of Ministers after giving in writing the decision of their party that they were abstaining, the petition said.
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The petitioner said the chief minister had described the action as unprecedented.
All these constituted lack of collective cabinet responsibility, the petitioner said.
The CPI, second largest partner in the ruling coalition, had asked its four ministers to stay away from the meeting if Chandy attended it.
In her report to the state government, the Alappuzha collector had stated that large-scale violations of Kerala Land Conservation Act and Conservation of Paddy land and Wetland Act had been committed by the resort.
Meanwhile, a separate petition was also filed for a direction to the chief minister, not to permit the participation of the CPI ministers in evolving important policy decisions in view of the "commission of breach of oath" taken by them under the constitution.