Fiji's military has asked the police commissioner, Andrew Hughes, to step aside amid disagreements over the military's removal of a consignment of ammunition from the port in Suva.
The ammunition was removed without getting the required import authorisation from police which held it back for security reasons.
Navy Captain Esala Teleni, who was the acting commander until Commodore Frank Bainimarama returned to Fiji on Saturday, has confirmed that he wrote the letter to Mr Hughes.
The Pacnews news agency says he told Mr Hughes that if he insists that the military should be investigated for the removal of the ammunition, then in the interest of justice and fair play, he must step down.
Captain Teleni says the police commissioner cannot play the dual roles of being complainant and investigator at the same time.
Police have confirmed receiving the letter but declined to say whether Mr Hughes will respond.
Captain Teleni insisted however that Mr Hughes breached an understanding they had over the removal of the ammunition.
He says the Fiji military is also trying to verify suspicions that most of the personnel sent to the Australian high commission are members of the Australian elite SAS unit.