In Indonesia's Papua province, Human Rights Watch says police arrested more than 300 protesters at a political rally where separatists declared independence from Indonesian rule on Wednesday. Demonstrators also called for the closure of the local Freeport McMoran gold and copper mine, where operations have been halted by occasionally violent labor strikes. Locals in Papua province have long felt marginalized.

The unrest in Jayapura on Wednesday began when Indonesian soldiers fired warning shots into the air as high-profile West Papuan leaders declared their independence from Indonesia. Indonesian military forces beat protestors with rattan canes and batons outside the planned congress attended by 5,000 people.

Protestors at the congress also raised the controversial Morning Star Flag, a symbol of West Papuan Independence, and an act that carries lengthy jail terms.

Papua police announced Thursday that there were two fatalities from the independence rally, and that five suspects implicated in the riot, including some high profile Papuan independence leaders, have been charged with treason and possession of weapons.

Demonstrators also aired grievances about labor conditions at Papua's Freeport mine, which was temporarily closed after ongoing strikes and security concerns this week.

But Jakarta-based risk analyst Todd Elliot says there is no direct link between the labor movement and calls for independence in West Papua.

"I don't think there is a direct relationship between the congress and the labor problems at Freeport," said Elliot. "But I do I think they are both fueled by some underlying currents of native Papuans feeling marginalized and not treated fairly."

Papuan activist Dorus Wakum says that for many native Papuans, the government and Freeport have become synonymous with human rights abuses and growing inequality.

"Why has the congress declared that Freeport be closed? Because they see that Freeport don't give benefit[s to] the Papuan people. So it's a problem," said Wakum.

Yohannes Sulamain is a lecturer at the Indonesia National Defense University in Jakarta. He says the problems stem from a lack of education and corruption that siphons off much of the government budget, and stops Papuans from securing well-paid jobs at Freeport.

"There is huge corruption in the ministry of education," said Sulamain. "It makes the situation worse and worse. So I cannot really blame the Papuans for saying they are kind of pissed off with Freeport and the government, because they don't see the government do anything for them, they don't see them care enough about the locals."

Wednesday's Papuan congress was the third of its kind. The last one was held more than a decade ago.

West Papua is one of the poorest regions in Indonesia, but the province also has a wealth of natural resources. Separatists have called for independence from Indonesia for decades and while the province has been granted special autonomy, West Papua remains a sensitive issue.

The central government in Jakarta has yet to make a statement about the congress, a response that analyst Todd Elliot says is characteristic of the current government's approach to Papua.

"I think what is noticeable is the lack of response from the Indonesian government," added Elliot. "There has been a noticeable lack of attention to Papua in the current administration and the previous Yudhoyono administration despite calls from a number of people, including some prominent current and former officials and ministers urging for peaceful dialogue and resolution to the problems in Papua. Things happen and you don't hear anything from the state palace or anyone."

The five suspects charged with treason and possession of weapons face between six and 20 years in prison.