New Zealand and the Cook Islands are not seeing eye to eye on a number of issues, the Foreign Affairs Minister's office says.
The Cook Islands is set to discuss a major partnership agreement with China this week.
A spokesperson for Deputy Prime Minister Winston Peters told RNZ that the lack of transparency with other countries could have significant security implications.
"We can confirm that there are a number of issues on which New Zealand and the Cook Islands Government currently do not see eye to eye," the spokesperson said.
"These include the proposal for a separate Cook Islands passport, the Cook Islands shipping registry, and 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 Cook Islands operates in free association with New Zealand. It means the island nation conducts its own affairs, but Aotearoa needs to assist when it comes to foreign affairs, disasters, and defence.
Peters' spokesperson said New Zealand had 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.
"We have also 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."
According to a 1News report, Cook Islands Prime Minister Mark Brown is travelling to China with a delegation on Friday and is expected to sign the agreement in Beijing.
He told the news outlet that his country needed to "look at other ways" to have a sustainable economy and partnering with "like-minded countries" is an important way to "maintain our prosperity levels".
In December, China's Executive Vice Minister of Foreign Affairs visited the Cook Islands and just last week so did New Zealand's China Ambassador.
Cook Islands Foreign Secretary Tepaeru Herrmann said the ambassadors visit was another opportunity to see where the Cook Islands and China can co-operate.
The Cook Islands this year is celebrating 60 years of free association with New Zealand.
Brown has continued to float the idea of a Cook Islands passport as part of the celebrations, which he originally called an "internal matter".
However, a spokesperson for Peters said the Cook Islands could only have its own passport if it became independent. It would mean Cook Islanders would give up their New Zealand passports, which entitle them to live and work in the country.
On Christmas Day, a Cook Islands flagged vessel carrying Russian oil was seized in Finland.
It is suspected to be part of Russia's shadow fleet and cutting underwater power cables in the Baltic Sea near Finland.