The state government had aqppealed against a Thrissur Vigilance Court order dismissing its application to withdraw the case.
The Supreme Court in September last year had asked the high court to dispose of within three months the appeal filed by the government.
The case related to import of palm oil during 1991-92 at 'inflated' price by the then Congress Government headed by late K Karunakaran from a Malaysian firm allegedly causing a loss of Rs 2.33 crores to the state exchequer. Chief Minister Oommen Chandy was the Finance Minister then.
The present government had decided to withdraw the case stating that the import had neither caused any loss to the exchequer nor had anyone made any unlawful gain from it.
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Dismissing the appeal, Justice P Ubaid in his 62-page judgement held "withdrawal from prosecution will not serve any public interest and no public good was going to be achieved by such withdrawal".
Besides the state's petition, the court also passed orders on three other connected petitions.
It rejected a plea by senior IAS officer, Giji Thomson, former SAI Director, who is tipped to be the next Chief Secretary, to quash the proceedings against him.
The court held that there is absolutely nothing to indicate that present prosecution is an 'abuse of legal process'. The request made by the petitioner cannot be allowed, it said.
The other two petitions were filed by Leader of Opposition in the state Assembly V S Achutanandan and CPI MLA V S Sunil Kumar seeking to implead themselves in the withdrawal plea by the state and the court held they have the right and locus standi to object withdrawal of prosecution as representatives of people.