Australia's foreign minister, Alexander Downer, says his meeting with Fiji's military commander today will be about security and defence cooperation, and not politics.
Mr Downer, who is on an official visit to Fiji, says he does not consider Commodore Bainimarama a politician.
Radio Fiji says Mr Downer made the comments in response to questions about why he will meet the military commander and not the home affairs ministers responsible for the military, Josefa Vosanibola.
But Mr Vosanibola believes he should have been consulted about Mr Downer's meeting with Commodore Bainimarama.
Fiji's foreign ministry says the meeting would take place because Mr Downer had requested it.
Meanwhile, Mr Vosanibola is also questioning why the opposition leader, Mahendra Chaudhry, met with Commodore Bainimarama to discuss security issues on Monday when he should have gone through the ministry.
But Mr Chaudhry says Mr Vosanibola does not know what he is taking about and does not know how a democracy works.