Indonesia has lodged a formal protest with Britain after a UK-based separatist leader announced an interim government-in-exile for the restive Papua province.

Mineral-rich Papua, Indonesia's easternmost province, has been dealing for decades with a low-level separatist insurgency, as well as poverty and communal tensions.

Benny Wenda, leader of a pro-independence group, this week declared himself the president of a new interim government in Papua, but an infuriated Jakarta dismissed his claim.

Indonesia's foreign ministry on Friday summoned British ambassador Owen Jenkins to convey "strong protest" over Benny Wenda's statements and activities, according to ministry spokesman Teuku Faizasyah.

"The British ambassador promised he would deliver Indonesia's strong protest and he also reiterated the UK government stance on the sovereignty and unity of Indonesian regions," he said in a statement on Saturday.

The British embassy did not comment.

Indonesia took control of Papua, a former Dutch colony, in the 1960s after a vote -- widely viewed as rigged -- showed a majority favoured staying under Jakarta's rule.

Wenda, who has been living in Britain since the early 2000s, leads one of the groups campaigning for Papua's independence, and Jakarta has declared that he is no longer an Indonesian citizen.

Indonesian security forces tasked with crushing the Papua rebellion have long been accused of committing atrocities against Papuan civilians.

The impoverished region has also seen communal and ethnic violence in recent years.

A spokeswoman for the UN Human Rights office said Monday the organisation was "disturbed by escalating violence over the past weeks and months" in Papua.