The ACP Council of Ministers in Brussels reportedly heard a joint statement on Papua from seven Pacific countries - Vanuatu, Solomon Islands, Tonga, Tuvalu, Nauru, Palau and the Marshall Islands.
The statement condemned Indonesian human rights violations in Papua and called for a resolution supporting the right of West Papuan political self-determination.
However, Indonesia's embassy in New Zealand says the ACP agreed in April that the group would not cover the issue of Papua in future meetings.
It has rejected reported claims from a Vanuatu minister that African and Caribbean countries support their push for a new Papuan self-determination process.
It said that in its response to Indonesia's embassy in Brussels, the ACP Secretariat rejected reportage of the Pacific statement, indicating the issue of Papua "did not feature" during the meeting.
Vanuatu's government envoy Johnny Koanapo was reported to have delivered the joint statement to the Council, warning that "apartheid-like colonial rule" was wiping out West Papuans as a people.
Mr Koanapo has said that the discussion set up the likelihood of a resolution on the full range of West Papua issues at the next ACP ministerial council meeting, scheduled for November.
However the Indonesian embassy has dismissed his statement.
"The argument made by a Vanuatu politician that African countries support self-determination in Papua is false," said the embassy in a statement.
"As close partners sharing common history and future, Indonesia and Africa have long expressed solidarity and full support towards each other's sovereignty."
According to the embassy, Indonesia enjoyed excellent relations with Pacific countries.
"The overwhelming majority of Pacific countries have no agenda to push for the separation of sovereign territories of Indonesia," it said.
"Calls to redraw the borders of Indonesia by a few politicians in Vanuatu, Solomon Islands and elsewhere, are simply crazy and irrational talk. These absurdities are talks of desperate and vulnerable political leaders clinging to stay in power."
The embassy said significant progress had been made by Indonesia in recent years in the areas of human rights and development in the provinces of Papua.
It said this was witnessed directly by several Pacific Islands' foreign ministers during their visit to Indonesia in 2014.