Principal District and Sessions court Judge Nazir Ahamed said investigation was at a preliminary stage and hence bail cannot be granted.
Krishnamurthy was arrested on charges on graft and abetting the suicide of the agriculture engineering department Assistant Executive Engineer S Muthukamaraswamy.
He was arrested on April 4 along with a Chief Engineer in the Agriculture Department, Senthil, who too faces similar charges.
Senthil's bail plea was dismissed by the judge last week and he has moved the Madurai Bench of the Madras High Court.
Muthukumarasamy jumped in front of a train after pressure was allegedly exerted on him over recruitment of seven drivers.
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