The Fiji army spokesman at the time of the coup, Lt Col Filipo Tarakinikini, has been ordered to return from New York and help with coup investigations.
The military spokesman, Captain Neumi Leweni, has told the Daily Post the commander in chief, President Iloilo, has not accepted Lt Col Tarakinikini's resignation and he has been declared a deserter.
The officer had resisted orders to return to Fiji by attempting to resign while in New York, but this was turned down by President Iloilo, whose decision was supported by the courts.
Captain Leweni says it would be inappropriate for Lt Col Tarakinikini to defy the president's orders, but if he does, the military may seek assistance from Fiji police and Interpol to bring him home.
As a deserter, he faces immediate arrest by military police.
Lt Col Tarakinikini went to New York at the beginning of 2001 to work for the United Nations but is now reported to be employed by a private security firm.