Ever since Indonesia achieved independence in 1949, the Jakarta government has faced a constant battle to keep the nation's 13,000 islands together.
Click on the map below for some of the main areas of conflict.
Papua, formerly known as Irian Jaya, has been dogged by secessionist violence ever since Dutch colonial rule formally ended in 1962.
Many Papuans saw the Dutch departure as a chance for complete independence. But within a year, forces from Jakarta had annexed the region and claimed it as part of Indonesia.
A low-level guerrilla organisation called the Free Papua Movement has been fighting a secessionist battle ever since.
Clashes between locals and security forces are an ongoing problem
Despite a heavy Indonesian military presence, attacks and skirmishes have occurred throughout the last four decades, killing thousands of Papuans.
The situation has been exacerbated by tensions within the Papuan community.
Locals - who are mainly Christians or Animists of Melanesian origin - have clashed with Muslims who moved to the region as part of the government's transmigration programme.
The Dutch colonised Papua in 1828, but unlike the rest of Indonesia, they did not relinquish control of the province until the 1960s.
Instead, on 1 December 1961, they agreed to grant Papuan self-rule.
When the Dutch left, they handed Papua over to the United Nations and then to Jakarta, in a transfer agreement which stipulated that Papuans would be able to decide within six years whether to accept incorporation into Indonesia.
This opportunity came and went - and many Papuans, as well as human rights groups, have questioned why the region has still not been allowed a vote for independence.
PAPUA: KEY FACTS
Formerly known as Irian Jaya, it is Indonesia's poorest region
Majority of population is Melanesian
Shares a border with Papua New Guinea
Annexed by Indonesia in 1963
Separatist campaign since 1960s
From the time Jakarta first annexed the province, there have been sporadic clashes between independence supporters and security forces.
When President Suharto left office in 1998, advocates of Papuan separatism renewed their call for independence.
Abdurrahman Wahid came to power in October 1999 and attempted to de-fuse the situation by publicly announcing that the government should accept the blame for some of the region's difficulties.
But Papuans still had many grievances against Jakarta. A major complaint was that much of the revenue from the region's extensive mineral and oil resources was going to central government coffers, rather than benefiting local people.
In 2001 Jakarta tried again to appease the Papuans, by granting them greater powers to manage their own affairs.
The region was allowed to keep up to 80% of the profits from its sale of minerals and agricultural produce, and was also allowed to change its name from Irian Jaya to the locally-preferred name of Papua.
But despite these concessions, the situation remains volatile.