The New Zealand High Commission in Nuku'alofa says the $1.36 million 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 did identify poor record-keeping, Radio New Zealand International reports.
The high commission says that led to some money being inadvertently used for other government purposes.
It says the balance of New Zealand funds were returned to New Zealand on Wednesday. The statement does not say how much has been reimbursed.
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.