Indonesian security forces and West Papuan activists have clashed during protests to mark the 50th anniversary of the province declaring independence.

Local television stations showed footage of police driving through crowds of protesters who were waving Papuan independence flags and cheering.

The footage showed police firing shots into the air, violently wrestling protesters to the ground, and confiscating the province's banned independence flag.

There are also reports protesters were shot but this cannot be confirmed as the ABC is not allowed into the region.

TV reports also showed images of an Indonesian policeman who it is claimed was shot with an arrow during the clashes.

Many West Papuans were arrested when the province held independence ceremonies in December 2011. ( Reuters: Muhammad Yamin )

The disturbances happened on Thursday at rallies marking the 50th anniversary of West Papua's declaration of independence.

That declaration is not recognised by Indonesia and the Australian Government says it respects Indonesia's sovereignty over West Papua.

Police said they fired warning shots but Indonesian security minister Djoko Suyanto denied that protesters had been shot.

He said protesters attacked a policeman and a number of Papuans were arrested for waving their independence banner.

The head of the West Papua Baptist Church, Reverend Socrates Yeoman, says several people taking part in the flag-raising ceremonies were shot and others arrested by Indonesian security forces.

Video on YouTube has also shown flag-raising ceremonies being conducted in Papua on November 30.

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Reverend Yeoman says security has been tightened, with increased numbers of police and military.

He says despite the violence he and his compatriots will continue their activities.

"We are here. How can they do this? We are the owners of this land. How can these outside people be coming in and killing, arrest and torture us continually?" he said.

Foreign journalists are not allowed into the region so it is difficult to verify the many reports coming from there.

Flag-raising ceremonies were held in a number of towns across Papua, while in Jakarta where Papuans in traditional dress marched through the streets of the capital.

Others ceremonies were held overseas in Australia, New Zealand and the Netherlands.