An investigation is being held into whether Relationships Aotearoa fudged the number of clients it had to get more Government funding.
The country's oldest counselling service was forced to close earlier this month, after funding negotiations with the Government broke down.
Social Development Minister Anne Tolley said liquidators were looking into discrepancies in numbers of clients and staff at Relationships Aotearoa.
"There's a large amount of taxpayer money that's gone into this organisation, and that was to fund services to a certain number of clients, and there doesn't seem to be that number of clients that they were talking about," she said.
"But it's still early days and we're waiting on the information from the liquidators."
Ms Tolley said Relationship Aotearoa's records were a mess.
John Fisk, from interim liquidator PricewaterhouseCoopers, told Checkpoint it was at an early stage but it was investigating concerns over an absence of files for thousands of clients.
"It was raised with us on Friday that there seemed to be a discrepancy between the numbers being quoted by RA [Relationships Aotearoa] before our appointment - of about 7000 clients, active ones - and what's been found by Stand, the agency that's working with MSD [the Ministry of Social Development], which was about 1000 active clients."