In a direct challenge to Jakarta, the demonstrators are calling for a new referendum on independence.
The rallies also mark the rise of younger activists impatient with the lack of progress over decades of demanding a fairer deal from Indonesia.
Presenter: Karon Snowdon
Speaker: Victor Yeimo from the West Papua National Committee; Camilia Webb-Gannon, Coordinator of Sydney University's West Papua Project
SNOWDON: On May 1st 1963 the United Nations handed over the administration of Papua to Indonesia.
The legality of the notorious Act of Free Choice in 1969 which resulted in Papua becoming a province of Indonesia through the vote of just one thousand Papuans has been challenged since then.
Rally organiser Victor Yeimo says this year's peaceful rally in the capital Jayapura attracted 20-thousand, a figure it's not possible to verify.
YEIMO: I report to you direct from the demonstration in Jayapura in West Papua. And they make a statement to support international law for West Papua, international parliament for West Papua, and they commit to demand a referendum in West Papua because Indonesia, Dutch and US have stolen our right of self determination through the "Act Of No Choice" in 1969.
SNOWDON: The rallies marked the day with placards, speeches and dances. They had official permission but there was a strong police and military presence.
Camillia Webb-Gannon is the Coordinator of the West Papua Project at Sydney University's Centre for Peace and Conflict Studies.
She says the younger generation is taking the reins, fed up with what it regards as the failure of previous leaders to achieve any change through years of diplomacy and dialogue.
WEBB-GANNON: For the past four decades this movement has been run by the older generations who are now becoming according to the current generation of students more obsolete in their methods. While they think they can be effective in some circumstances they haven't been for West Papua. So today they are focussing on using civil resistance and mass protests. And I think this rally really carries on from last June and July, the mass rallies they held then in Jayapura where up to 20,000 people were protesting.
SNOWDON: And if they think that the older generation's methods of negotiation and diplomacy have failed does that mean they are advocating more militant action or even armed conflict or anything like that?
WEBB-GANNON: No definitely not. The KNBP which stands for the Komite Nasional Papua Barat or the National Committee of West Papua, is the main student and youth movement that's active today. And they look to people like Gandhi and other revolutionary movements using civil resistance and people power.
SNOWDON: Controversially, the movement has rejected the special autonomy granted by Jakarta that was meant to address some of the Papuans' grievances.
These include military violence, arrests, torture, Indonesian migration and a lack of development.
They want nothing less than full independence from Indonesia, calls for which usually lead to jail.
Victor Yeimo says a new UN sponsored referendum should be organised.
YEIMO: And there are so many, many people they want to show to the international and Indonesia for the international (community) facilitate a referendum as the solution in West Papua.
SNOWDON: A referendum for independence, is that what you're demanding?
YEIMO: Yes and we want to choose what we want. We want independence through a referendum solution.
SNOWDON: Camilia Webb-Gannon believes despite the media bans and other restrictions imposed by Indonesia, the Papuan cause will in future attract the international attention it now lacks.
WEBB-GANNON: And I think that it's becoming an increasingly important international issue because of the use of new technology and social medias and Utube and videos. But that's more of a recent thing because media is changing. But I think its going to be hitting the international agenda a lot harder in coming years.