The New Zealand high commission in Nuku'alofa says the 1.36 million New Zealand dollars provided to Tonga's Constitutional and Electoral Reform programme has been accounted for.
In a statement, it says an independent audit found no evidence of fraud in the programme but identified poor record-keeping leading to some money being inadvertently used for other government purposes.
It says the balance of New Zealand funds were returned to New Zealand yesterday.
The statement doesn't say how much was reimbursed.
The High Commissioner, Jonathan Austin, says the Tongan authorities' investigations into the use of Government of Tonga money in the Prime Minister's Office is a matter for them.