The Australian Government has expelled Fiji's top diplomat in response to a decision by the country's military leaders to declare Australia's High Commissioner persona non grata.

Foreign Affairs Minister Stephen Smith announced the Government's decision after considering a range of options overnight.

Fiji's military ruler, Commodore Frank Bainimarama, told the Australian High Commissioner he had 24 hours to leave the country after accusing Australia and New Zealand of interfering in judicial appointments.

Mr Smith said the Fiji Government was formally advised that its Acting High Commissioner in Canberra, Kamlesh Kumar Arya, had been expelled and had 24 hours to leave the country.

"This is deeply regrettable and Australia is deeply disappointed at Fiji's conduct in this matter,"" he said.

Mr Smith said he had also spoken with his New Zealand counterpart Murray McCully, who has also ordered Fiji's top envoy out of the country. "About this time in New Zealand he is announcing that New Zealand is taking comparable action in response to the declaration of the New Zealand Deputy High Commissioner as persona non grata," he said.

Mr Smith has rejected Fiji's claim that Australia has been meddling in its judicial affairs. "This excuse is neither warranted, reasonable, nor justified and regrettably it takes Fiji's relationship with Australia, Fiji's relationship with New Zealand, Fiji's relationship with the Pacific Island's Forum and Fiji's relationship with the international community backwards," he said