The Cook Islands Treasury says it is working to resolve a backlog of unaudited accounts from 2013.
The operations manager of the Cook Islands Treasury, Tiu Tiulilo, said a new accounting system would soon be introduced across the government to address the problem.
"The current situation is that each of the 44 government entities, they use their own system, do their own reporting and that's part of the issue that we've identified," he said.
"When the audit goes in they are missing information or [have] incorrect reporting."
Government accounts had been audited up to 2017 and state-owned-enterprises up to 2018, Mr Tuililo said.
But because they had been done separately and work had not been "up to standard", all audits now needed to be consolidated before they could be signed off by the Finance Minister, he said.
The new accounting system was due to be launched in February or March next year and the government's consolidated audits should be up to date within the next two years, the operations manager added.
"It's an integrated system where everyone will use the same system, all the processing we do through the same system and the recording will be improved significantly."