A bench of justices A K Patnaik and J S Khehar considered the plea of the state government and kept the petition of Thomas pending saying that if required, his plea would be heard after the Commisison of Inquiry and the trial court decides the application (of Kerala) seeking withdrawal of case.
"We make it clear that the pendency of this matter will not come in the way of decision of the Commission of Inquiry and the trial court," the bench said, adding the outcome of the proceedings below be intimated to it after eight weeks.
"He acted as per the decision of the cabinet. He is now a retired civil servant and now will have to engage lawyers," senior advocate Harish Salve said, adding "even the CVC has said that there is no case of prosecution against him."
"Whenever there is a change in the regime, the case comes up," he said.
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The Supreme Court had in 2011 allowed Kerala government to go ahead with the trial in the case.
The case against the then chief minister K Karunakaran got abated due to his death.
The apex court had on August 3, 2007 stayed proceedings in the case before a designated CBI court in Kerala. There were eight accused in the Palmolein import case.
The case pertains to import of palm oil from a Singapore firm, which was allegedly done at prices higher than the international rate.