Both men have pleaded not guilty to one count each of abuse of office.
RNZ Pacific reports Magistrate Seini Puamau has set bail at $FJ10,000 (over $NZ7,000), according to local media reports.
Bainimarama and Qiliho have also been ordered not to leave the country and to reside at a permanent address.
Magistrate Puamau also ordered them not to interfere with witnesses.
They are next expected in court on May 11.