The region has been the scene of violence and tension in 2012, with independence leaders arrested, beaten and killed, and police confronted by unruly and angry demonstrations.
In June, Indonesian soldiers went on a rampage in the highland's town of Wamena, a stronghold of the West Papua National Committee, which is known as KNPB.
Last weekend police were again targeting the area, raiding the homes and offices of KNPB members.
Eight people were arrested and witnesses, including KNPB leader Victor Yeimo, say once again the Australian-trained and funded police unit Detachment 88 was involved.
"When they arrest the KNPB brothers in Wamena, we saw Detachment 88 with one car, and another car with police, joined in by TNI (the Indonesian military)," Mr Yeimo said.
Indonesian police accuse those arrested of making bombs and claim to have found explosives during the raid.
Mr Yeimo rejects that and says his group is being framed as terrorists to justify Detachment 88's presence.
In West Papua, the Institute for Human Rights Advocacy, known as ELSHAM, has studied the arrests and suspects the explosives recovered by police were planted.
It is a view that is supported in Australia by advocates of the West Papuan cause.
"They don't have the capacity to gain the materials, so ELSHAM has actually said that the material was probably planted in the KNPB member houses where they found the explosives, and that's not an unusual thing for security forces to do," says Cammi Webb-Gannon, from the University of Sydney's West Papua project.
"I don't think KNPB has any reason to be making bombs because they believe in a peaceful approach to pursuing independence, they want a referendum on independence in West Papua."
Deadly crackdownsDetachment 88, which is trained by Australia as part of counter-terrorism operations, has also been linked to a string of incidents in which Papuan independence leaders have been arrested and killed.
When 7.30 travelled to the province in August, the crackdown on the independence movement was already severe and had resulted in several deaths, including the killing of former KNPB leader Mako Tabuni.
Witnesses say he was shot in a street by Detachment 88.
Victor Yeimo succeeded Mr Tabuni as leader of the KNPB and since then, he says the crackdown has worsened as he takes the campaign public.
"We are the non-violent activists in West Papua," he says in a video sent to 7.30.
"We will fight for our right of freedom according to peaceful means in West Papua.
"We demand our right of self-determination, for referendum to be held in West Papua peacefully and democratically."
But the Indonesian authorities do not believe his claim of non-violence and they are pursuing KNPB like never before.
International observers say it is because the Indonesian government is threatened by the movement.
Cammi Webb-Gannon says the Papuan movement's international links could explain Indonesia's concern.
"First of all a lot of them are young, they're students, or have recently been students," she told 7.30.
"So they do have a lot of passion, a lot of fire, they have a popular support base, they work from a very grassroots perspective, and I think Indonesia is worried because they do have these international links."
New police chiefThe weekend raids follow the appointment of a new police chief in Papua, Brigadier General Tito Karnavian.
His background as the former head of Detachment 88 generates serious unease among some Papuans despite his assurances of a new inclusive approach.
"They will be opposed to his former role as head of Densus (Detachment) 88, and as a police chief it doesn't seem to mesh with his new approach of working to win the hearts and minds of Papuans," Ms Webb-Gannon said.
7.30 put several questions to the Indonesian government about the latest situation in Papua but received no reply. Attempts to contact the new Papuan police chief were also unsuccessful.
As for Mr Yeimo, he is pushing for the release of the eight activists arrested on the weekend.
And with his supporters in Australia, he is pressuring the Australian Government to rethink its funding for Detachment 88.
"The Papuans will be pretty much living like prisoners in our own land, where our movement, what we do will be censored, will be followed, will be monitored," Mr Kareni said.
"There's no room for democracy at all."