RNZ reports the accusation during the UN General Assembly came after leaders from six Pacific countries - Vanuatu, Solomon Islands, Tonga, Nauru, the Marshall Islands and Tuvalu - expressed concern about human rights abuses in Papua.
Calls for Papuan self-determination rights to be respected were also made by some of the leaders during this 71st session of the general assembly debate.
"Human rights violations in West Papua and the pursuit for self-determination of West Papua are two sides of the same coin," said the Prime Minister of Solomon Islands, Manasseh Sogavare.
"Many reports on human rights violations in West Papua emphasise the inherent corroboration between the right to self-determination that results in direct violations of human rights by Indonesia in its attempts to smother any form of opposition."
In a call echoed by the other Pacific leaders, Marshall Islands President Hilda Heine urged the UN Human Rights Council to initiate a credible investigation of violations in West Papua.
While Indonesia's Vice-President, Muhammad Jusuf Kalla, did not address Papua in his speech at the session, Jakarta's response to Pacific governments' criticism came from an official at Indonesia's permanent mission to the UN.
Nara Masista Rakhmatia said her government was shocked to hear the island countries' claims about Papua when discussion at the session should have been about sustainable development goals and the global response to climate change.
"The same leaders chose instead to violate the UN charter by interfering in other countries' sovereignty and violating its territorial integrity," she said.
She said her government categorically rejected accusations of rights abuses in Papua, and that they reflected an unfortunate misunderstanding of the history of Indonesia and its current progressive developments.
Ms Rakhmatia singled out Vanuatu and Solomon Islands in particular, suggesting other countries with human rights problems shouldn't point the finger at Indonesia.
"Their politically motivated statements were designed to support separatist groups in the said provinces [West Papua and Papua] who have consistently engaged in inciting public disorder and in conducting armed terrorist attacks."
The official reiterated Jakarta's stand that it had mechanisms in place to deal with human rights abuses in Papua.
"With such a vibrant national democracy, coupled with the highest commitment to the promotion and protection of human rights at all levels, it would be nearly impossible for any human rights allegations to go un-noticed and un-scrutinised," she said.
Jakarta, however, maintains restrictions on access to Papua for leading international humanitarian and rights organisations such as the International Committee of the Red Cross and Amnesty International.
Furthermore, Indonesian police chiefs in Papua region have taken a strict line on a series of large, peaceful demonstrations by Papuans calling for self-determination in recent months, resulting in mass arrests in some cases.
The prime minister of Tuvalu, Enele Sopoaga, said that the UN could not and must not ignore the "deplorable situations" in Papua by hiding "behind the guise of the principles of non-interference and sovereignty".
"The UN must act on this issue and find a workable solution to give autonomy to the indigenous peoples of West Papua," he said.