The 34th regular session of the UN Human Rights Council in Geneva, Switzerland, was told that Indonesia has not curtailed or halted various widespread violations.
Vanuatu's Justice Minister Ronald Warsal was speaking on behalf of his country and six other Pacific nations: Tonga, Nauru, Palau, Tuvalu, the Marshall Islands, and Solomon Islands
"We note that in the past 15 years, the Indonesian National Commission on Human Rights has collected evidence of gross human rights violations by Indonesian security forces in three principle areas of West Papua: Wasior, Wamena and Paniai."
Mr Warsal said the Commission described the sets of cases in the first two places as crimes against humanity, which are punishable under Indonesian and international laws.
He referenced reports of extrajudicial executions of activists and the arrests, beatings and fatal shootings of peaceful demonstrators, including high school students; as well as persistent violence against Papuan women.
The Vanuatu minister said Indonesia's government had not been able to deliver justice for the victims.
"Nor has there been any noticeable action to address these violations by the Indonesian government, which has, of course, immediate responsibility and primary accountability," he said.
He also mentioned the marginalisation of West Papuans in the face of steady migration to the region by people from other parts of Indonesia.
"We want further to highlight another broad aspect of human rights violations - the Indonesian government policy over many decades and continuing until today of the migration of non-indigenous Papuans to West Papua, leading to a dramatic decline in the percentage of the indigenous Papuan population."
Denial by Indonesia
Indonesia's delegation to the UN mission in Geneva has issued a reply, saying it categorically rejects the allegations voiced by Vanuatu's Justice Minister.
It said Mr Warsal's address does not reflect the real situation on the ground, accusing Vanuatu of "using human rights issues to justify its dubious support for the separatist movement in Papua".
In a statement, Indonesia said its record on the promotion and protection of human rights spoke for itself.
"This includes our co-operation with various UN Special Procedures and Mandate Holders, as well as various collaborative endeavours at bilateral, regional and multilateral level including within the Human Rights Council in strengthening human rights mechanisms as well as in the promotion and protection of various basic human rights."
"As a matter of fact, this year Indonesia will welcome the visits of two Special Rapporteurs, and present our third UPR report this coming May."
Earlier, Mr Warsal referred to a series of recent pronouncements by mandate holders of the UN Council about serious Indonesian violations of the human rights of indigenous Papuans.
These included representations by UN Special Rapporteurs on the promotion and protection of the right to freedom of opinion and expression; the rights to freedom of peaceful assembly and of association; the rights of indigenous peoples; the Rapporteur on extrajudicial, summary or arbitrary executions; and the Rapporteur on torture and other cruel, inhuman or degrading treatment or punishment.
Indonesia's government, however, said it had always endeavoured to address any allegation of human rights violation as well as taking preventative measure and delivering justice.
The Indonesian government again sent a message to Vanuatu that it should stay out of what it regards as its own domestic matters.
Jakarta said that Vanuatu's government should not divert its focus from addressing its various domestic human rights problem by politicising the issue of Papua for its domestic political purposes.
"In this regard, the Indonesian Government is prepared to work and co-operate with the Government of Vanuatu in their efforts to address various human rights violation and abuses against the people of Vanuatu" said the statement.
These abuses, according to Indonesia, included "violence against women, corporal punishment against minors, appalling prison condition, including torture of prisoners, and other challenges".
However, the seven Pacific nations have called on the UN Human Rights Council to request the High Commissioner for Human Rights to produce a consolidated report on "the actual situation in West Papua".
Among other provisions, Mr Warsal said the report should also detail the various rights under the International Bill of Human Rights and the related conventions, including the right to self-determination.
"We believe that challenges of West Papua must be brought back to the agenda of the United Nations," said the Vanuatu minister on behalf of the Pacific countries.