Justice Nagamohan Das passed the order while dismissing the petitions filed by KFA and its chief Mallya.
A Special Economic Offences Court here had initiated criminal proceedings last year based on I-T Department's three separate complaints.
With the dismissal of petitions, the stay granted earlier by the High Court on criminal proceedings before the special court stands vacated.
Kingfisher Airlines owes over Rs 350 crore to I-T Department on account of alleged TDS defaults committed many years ago and has been held as an assessee in default from the original date of its failure to remit tax.
The airlines had deducted tax, hence the claim of the Department on the property also dates back to that period, according to the Department.