The Pacific Conference of Churches says donors and foreign governments must treat victims of disaster with dignity and not attach conditions to relief efforts.
The call coincides with this week's visit to Fiji of Indonesia's Co-ordinating Minister for Political Affairs, Law and Security, Luhut Binsar Padjaitan.
Mr Padjaitain is reportedly to give Fiji an assistance package worth up to 5 million US dollars and a contingent of engineers for the country's rehabilitation efforts in the wake of the devastation caused by Cyclone Winston last month.
PCC General Secretary, Reverend Francois Pihaatae, said Indonesia's offer should be welcomed but noted that Padjaitan's visit had glaring political overtones.
He noted the minister had been "extremely vocal against groups seeking self-determination in Papua" and had publicly called for West Papuan activists to be removed from the country.
Back in Jakarta, a senior government official told Indonesian media earlier this week that the ministerial visit was to suppress regional support for the United Liberation Movement for West Papua.
As the ULMWP was recently granted observer status at the Melanesian Spearhead Group, Jakarta has increased its diplomatic overtures to the region.
But Reverend Pihaatae said that any bilateral talks between Indonesia and Fiji on the issue of West Papua should not be influenced by assistance to cyclone victims.
"We call on all donors - including NGOs - not to attach conditions to their aid and to refrain from providing assistance along with a discreet message to support a political cause," he said.
The Reverend said that New Zealand and Australia - long seen as opponents of Fiji's prime minister Frank Bainimarama - had rushed to Fiji's aid following the cyclone, setting no pre-conditions for humanitarian assistance.
"By accepting conditional aid," he said, "regional governments do their people a great disservice."
Self-determination talk off limits
As part of his Pacific trip, Luhut Binsar Padjaitan is also to visit Papua New Guinea where he is due to arrive in Port Moresby tomorrow.
PNG's Foreign Minister Rimbink Pato indicated that talk of West Papuan self-determination remains off limits.
Mr Pato said that at the political level, PNG's relationship with Indonesia was at its peak, and people-to-people engagements are growing.
"For example, Papua New Guinea is, I think, the only country in the Pacific Islands that Indonesia has given free visas to. Every citizen from PNG can enter Indonesia without applying for visas," he enthused. "This is even better than visas on arrival."
But Rimbink Pato insisted his government considered West Papua an integral part of Indonesia and was committed to not discussing West Papuan self-determination.
"So we're not interested in entertaining the issue of self-determination, because that's never an issue for us, and that's never a concern for us."
Mr Pato said however that PNG would continue to discuss concerns over human rights issues in Indonesia's Papua region, pursuant to a resolution by the Pacific islands Forum last year at its leaders summit in Port Moresby.
Mr Padjaitain last week announced government intentions to have a number of human rights abuses in West Papua probed.
However, earlier this month the provincial government of Papua province urged the minister, a former military leader, to resist from making provocative statements that might cause anxiety in the region, after he signalled a hardline security forces response to a recent mulitple killing.