High Court judge Aditya Patabendige had issued the order after considering a revision petition filed by the accused over the case.
Mr. Fernando has been charged at the Colombo Magistrate's Court for deploying 153 employees of the Cooperative Wholesale Establishment for election campaigns between 2010 and 2014.
The Bribery Commission has alleged that this move had caused losses worth Rs 40 million to the government.
The accused had filed a revision petition seeking a court order ruling that the Magistrate's Court's decision to hear the case after dismissing his objections, is an unlawful one.
Further hearing of the petition has been fixed for October 09.