Indonesian security forces have banned any demonstrations in the restive provinces of Papua and West Papua following more than two weeks of protests demanding the region's independence.

Authorities cited security and public order reasons for the ban intended to prevent "anarchist acts" in a series of decrees published overnight following the arrest of several protesters on Sunday.

"Everyone is prohibited from participating in demonstrations or conveying their opinions in public that can carry with them anarchist acts, damages or the burning of public installations," the Papuan police said in a statement released via Twitter.

The latest wave of civil unrest in these two Indonesian provinces started in mid-August after 43 pro-independence Papuan students were arrested on the island of Java.

The students had reportedly received racist insults by nationalist Indonesians after the former allegedly desecrated the Asian country's flag.

According to official statistics, at least two protesters and a soldier have died in sporadic clashes during the marches - which were otherwise generally pacific in nature - while unofficial data from Papuan activists suggests the number of people killed is actually higher.

On Friday, hundreds of pro-independence demonstrators occupied the residence of the governor of Papua province and were later evicted without any violent confrontations.

Both provinces have witnessed a low-intensity secessionist armed conflict for decades.

Amnesty International has denounced the Indonesian armed forces' impunity in killings and heavy restrictions on access to the region for foreign journalists and academics.

Indonesian Papua occupies the western half of the island of New Guinea, a land rich in natural resources.

The pro-independence movement erupted in 1963, when the Netherlands withdrew from its last colonial possession in what was once the Dutch East Indies.

The eastern half of New Guinea is made up by the independent state known as the Republic of Papua New Guinea.