Mathew Batsiua and Squire Jeremaiah, who were opposition MPs at the time of the protest, had their passports confiscated when charges were laid.
On 13 September Justice Geoffrey Muecke granted a permanent stay on the charges faced by what had been dubbed the Nauru 19.
Mr Batsiua said both men have since sought the return of their passports, which he believes should have been done within about 48 hours but this hasn't happened.
He says the government may be using section 18 of the Passport Act to justify with holding the travel documents.
"It was to do with myself, or the applicant which is myself and Mr Jeremiahm, being a danger to the country we are travelling to.
"We don't believe that we are a danger. All that time we were in court, despite the lengthy time under bail- we never once breached out bail conditions. That's why we feel we have some grounds to appeal."