The governor of Port Moresby has raised the flag of the West Papuan independence movement, despite a request by Papua New Guinea's prime minister not to do so.

Police told several hundred West Papuan refugees not to march through Port Moresby's streets today but they did anyway, calling for independence from Indonesia.

Their destination was city hall, where governor Powes Parkop raised the Morning Star flag of the West Papuan independence movement.

"Papua New Guineans: for the last 50 years we have been silent, blind, not seeing, not hearing, not speaking. But tomorrow it must change," he said.

Prime minister Peter O'Neill had asked him not to raise the flag.

Also at the flag-raising ceremony was visiting West Papuan activist Benny Wenda and Australian human rights lawyer Jennifer Robinson.

The pair are in the Port Moresby at the invitation of Mr Parkop.

But PNG immigration officials have threatened to deport them for "engaging in political activity".

Ms Robinson says an official told her independence was a sensitive issue for Indonesia.

"I think it's a grave concern that Indonesia has such influence on domestic matters in Papua New Guinea," she said.