Vanuatu's foreign minister has demanded the Australian Federal Police (AFP) close its liaison office in the capital Port Vila because of disrespect towards the nation's prime minister.

Alfred Carlot has warned that AFP members in Vanuatu will be arrested if the Australian Government does not "take into account the decision of Vanuatu government" within 24 hours and close the office on Thursday.

Mr Carlot has asked the AFP to explain why Vanuatu's prime minister and delegation were required to complete immigration and customs clearances while they were in transit through Sydney Airport earlier this month.

He said the Australian High Commissioner was aware of his demand, which included the "closure of all AFP operations in various government law enforcement agencies in Vanuatu".

In a press release, Mr Carlot said the "concerns of the government are purely to do with the disrespect of the prime minister of Vanuatu".

He stressed they were not related to the arrest of Clarence Marae, the prime minister's private secretary, who was detained by the AFP at Sydney Airport over an alleged international tax scam.

Vanuatu's prime minister, Sato Kilman, has strongly condemned the manner in which the AFP arrested his secretary, Mr Marae, who is now in police custody in Brisbane.

The leader of the nationalist Nagriamel movement, Jeff Patunvanu, is calling for Australia to apologise.

"I think Australia should come out and apologise for what it has done," he said.

"We have expressed to our prime minister, that we want the prime minister to expel the Australian embassy and send all the AFP personnel and the officers who live in Vanuatu or work in Vanuatu ... we ask them to leave this country."

Foreign Minister Bob Carr has urged the Vanuatu government to reconsider its plans.

Mr Carr says the people of Vanuatu would be losing a valuable source of aid if Australian police are forced to leave.

"If Vanuatu had a grievance with what happened ... then I'd be happy to facilitate ways of expressing that grievance to save them any self-inflicted damage that expelling our federal police personnel might render them," he said.

In 2003, members of the AFP were forced to leave Vanuatu after facing accusations of spying and interference in Vanuatu internal affairs.