The Cook Islands arm of a United Nations NGO says a change to the way the country receives aid money could compromise the independence of the country's civil society organisations.
The acting finance secretary says the EU's backing a government push to have aid funding delivered straight into the general budget.
Teariki Rongo of the Global Environment Facility Small Grants Programme says both the government and donor partners will need to consult with NGOs as to the implications of such a change.
"The NGO's - we have to recognise their role in the community. And if a move like this is going to take away their independence so that they're being scrutinised by government in what they do that might defeat the purpose of the role of NGOs in the community."
Teariki Rongo says the role of NGOs complements that of the government and an aid change to general budget support may put that role at risk.