Wellington raised its concerns ahead of a reported state visit to China by the prime minister of the self-governing South Pacific nation, which has a population of about 17,000.
The Cook Islands has a "free association" agreement with New Zealand, which provides it with budgetary support and assistance on foreign affairs and defence.
But there are "a number of issues on which New Zealand and the Cook Islands government currently do not see eye to eye," said a spokesperson for Foreign Minister Winston Peters.
Those issues included "the lack of transparency by the Cook Islands in respect of policies and partnerships with other countries which could have significant security implications for the Cook Islands, New Zealand and the wider Pacific family", the spokesperson said in a statement.
China is vying for diplomatic, economic and military influence in the strategically important Pacific region, challenging the historic sway of the United States, New Zealand and Australia.
In December, the Cook Islands hosted Chinese Executive Vice Foreign Minister Ma Zhaoxu to discuss strengthening ties in areas such as economic development, health, education and responding to climate change.
Cook Islands Prime Minister Mark Brown's government said at the time that preparations were under way for him to make a state visit to China in 2025 and for both sides to finalise a "comprehensive statement of partnership".
A report by New Zealand broadcaster TVNZ on Wednesday said the prime minister would travel with a delegation to China on Friday and was expected to sign the agreement in Beijing.
- 'Security implications' -
The Cook Islands foreign affairs department did not immediately respond to a request for comment after office hours.
New Zealand did not specifically cite the proposed Cook Islands-China deal in its statement.
But it said Wellington had "emphasised that we would expect the New Zealand government to be fully consulted on any major international agreements that the Cook Islands plans to enter into that have major strategic and security implications".
Under the free association agreement with New Zealand, of which it was once a dependent territory, the Cook Islands' people are New Zealand citizens.
Though Cook Islanders are "integral members of the New Zealand family", the New Zealand foreign minister's spokesperson cited a list of concerns including a proposal for a Cook Islands passport and a Cook Islands shipping registry.
"New Zealand has consistently made clear to the Cook Islands that any major changes to the New Zealand-Cook Islands relationship, including policies which could entail the Cook Islands moving towards full independence from New Zealand, must be decided by the Cook Islands people via a referendum," the spokesperson said.
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