Dismissing the government's petition, Judge K Haripal held that withdrawal of the case was against public interest.
The government had decided to withdraw the case pertaining to alleged corruption and irregularities in the palmolein import deal, holding that it did not cause any loss to the exchequer nor had anyone made unlawful gain out of it.
The case had marred the careers of late Congress veteran K Karunakaran and former Central Vigilance Commissioner P J Thomas, who figured as accused in the charge sheet.
Apart from Thomas, IAS officer and Sports Authority of India Director General Jiji Thomson and former Civil Supplies Minister T H Musthaffa are among the eight accused in the case.
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The case pertains to alleged corruption in import of palmolein through a Singapore-based firm when Karunakaran was Chief Minister in 1992. Thomas was Civil Supplies Commissioner and Thomson the MD of the state Civil Supplies Corporation.
The case had haunted Karunakaran during his last stint as Chief Minister with the opposition as well as rivals in the Congress seizing on the issue to run him down.
The initial move to withdraw the case was made by Oommen Chandy during his first stint as CM in 2005 but it was reversed by the LDF Government headed by V S Achuthanandan that came to power in 2006.
After UDF came to power in 2011, it again decided to withdraw the case and filed a petition in the court in this regard.