It was a series of mass arrests across Papua province in the biggest clamp down by Indonesian police in more than a decade.
Over one-thousand protesters were detained in the provincial capital, Jayapura, hundreds more in other cities.
Those in Jayapura were held in an outdoor jail at police headquarters for eight hours before being released.
Chairman of the West Papua National Committee, Victor Yeimo, says many people were assaulted during the arrests.
"There's no room for democracy in West Papua, so they came suddenly to the place where we wanted to prepare for demonstration. And they arrested the people, they beat the people. This is peaceful action, we are the peaceful resistance. There are no torture there is no violence, but Indonesians give us the torture."
The protests coincide with the anniversary of the end of Dutch colonial rule in 1963, and a weekend visit by Indonesian President Joko Widodo.
Papua province - the western half of the island of New Guinea - has seen a long-running and often violent separatist conflict since being incorporated into Indonesia after a widely criticised UN-backed referendum.
Papuan journalist Victor Mambor says demands for a new referendum as an act of self-determination are viewed as treason.
"It's terrible for us. In my opinion it is not good for Indonesia (either). The problem is not about the welfare or the economic development, but the problem is the history."
Access to police headquarters has been blocked off to media, family, and advocacy groups, as up to 40 people remain detained.
Camellia Webb-Ganon from Sydney University think tank the West Papua Project says the arrests highlight Indonesia's heavy-handed approach.
She has called on the Australian government to pressure President Widodo over the matter.
"I'm surprised that such a large number of people would be detained for simply exercising their right to gather and to peacefully protest, because they have the right to gather to assemble and to peacefully protest for their other right: their right to self-determination."
Activists say the arrests will not stifle them, and have pledged to continue to publicly state their demands.
West Papuan independence leaders will today join parliamentarians, lawyers and humanitarian groups from the United Kingdom and the Pacific region in London to demand the United Nations pass a resolution for an independence referendum.
A spokesman for the Indonesian embassy in Canberra says he cannot verify the number of people arrested but believes it to be closer to 400.
He added police only intervened as protesters were breaking the law, but said if allegations of abuse are substantiated than the matter will be addressed.
