Greens leader Bob Brown has called for the resignation of Immigration Minister Amanda Vanstone after she accused Papuan separatists of racism.

Responding to an article by Senator Vanstone in The Weekend Australian newspaper, Senator Brown said the immigration minister had made a major gaffe in calling the cause of separatism "toxic" and based on "racist sentiment".

Writing about Papuan separatism, Senator Vanstone said in the article "Papuan nationalism in Indonesia" was based on hostility to people from other parts of Indonesia and was "racist sentiment" that should be condemned. "Separatism is a toxic cause that could, if encouraged, result in chaos, death and suffering on our doorstop," Senator Vanstone wrote.

Senator Brown described Senator Vanstone's comments as "despicable". "She is calling the cry for freedom toxic. She is calling the call for separation, that is independence, racist," Senator Brown said.

"It is a despicable way to be labelling the right of more than one million Papuans to an act of free choice. It is enormous misbehaviour from the minister for immigration," he said.

"The prime minister should have her job. She should resign over this. "This is inexcusable and it will have people shaking their heads right around the world. The reference to separatism as toxic means the Tibetans, the Kurds who want independence, the East Timorese, the Taiwanese are toxic," Senator Brown said.

Senator Brown said Ms Vanstone had a "one-sided view" that showed she was incapable of making independent judgments about Papuans' right to seek asylum in Australia.