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The refusal places Education Minister Hekia Parata in a tight spot - her officials have said the person should be identified.
The payment was one of a cluster of issues identified in the EY (Ernst & Young) report into Te Kohanga Reo National Trust. The report did not deal with the allegations which sparked the inquiry - they were ruled out of bounds.
But the $50,000 payment was inside the review's limited remit and it was identified among a number of credit card and koha rule breaches. The problems were singled out in a briefing note from the Ministry of Education to Ms Parata.
Early childhood education general manager Karl Le Quesne said the trust "was required to disclose this payment in their 2012 annual report".
Ms Parata's office did not return calls to say whether she backed her officials' view.
But the trust's spokesman, Derek Fox, said the trust would not reveal which of its board members got the payment.
He said it was a payment to a board member who had worked "well above the call of duty"on its successful claim to the Waitangi Tribunal.
"It wasn't a related party transaction - it was a koha," said Mr Fox.
Fresh claims of misspending by the trust have been referred by Ms Parata and Maori Affairs Minister Pita Sharples to the Serious Fraud Office, though some are questioning why it took so long to target the source of the original allegations.
The SFO will look at the trust's commercial wing, Te Pataka Ohanga.
It came after an unnamed trustee wrote to the ministers with new allegations about the trust's spending which Ms Parata said she could not ignore.
The SFO inquiry came after the release of an independent audit on Monday evening, which found no misuse of public money by the trust. The EY audit did not look at spending by Te Pataka Ohanga because it was deemed a private organisation.
Prime Minister John Key, in China, said Ms Parata was right to take the issue "very seriously"because it related to the spending of taxpayers' money.
The case originally came to light on a Native Affairs programme which detailed the subsidiary's spending on a wedding dress, a Trelise Cooper dress and cash withdrawals for the general manager's daughter.
Ms Parata said it was a third party which the Government had no power over.
Labour leader David Cunliffe said he did not accept this argument.
- Isaac Davison and David Fisher of the New Zealand Herald