The court's action came after it took cognisance of the offence under sections 276B and 278B of the I-T Act, 1962, for not remitting Rs 74.94 crore deducted as TDS in 2009-10 fiscal and Rs 23.70 crore imposed as interest for not meeting the deadline stipulated for payment.
Section 276B entails rigorous imprisonment for a minimum of three months and a maximum of seven years with fine.
The development spells fresh trouble for Mallya, whose airline is tottering with a net loss of Rs 755.17 crore for the third quarter ended December 31, 2012, a period when it did not operate a single flight.
The I-T officials on Tuesday had filed the criminal complaint against the airline and Mallya for failure to remit TDS for the fiscal 2009-10.
The I-T Department had also complained that Kingfisher owed the government Rs 401 crore as TDS amount, deducted from salaries of its employees and from payments made to others in the financial years 2008-2012.
The next hearing will be on April 19.
Carrying a debt of nearly Rs 8,000 crore and accumulated loss and liabilities of a similar amount, Kingfisher has been grounded since October 1 last year after its pilots and engineers went on a strike over non-payment of salaries.