He said the issues were historical, some dating back to 2012. If the investigation found possible criminal actions, police would be brought in.
The Health Ministry undertook a financial review of the trust in March and a governance review this month, after concerns were raised last year.
"The reviews didn't raise any specific concerns about their financial practices, but the auditors identified there was a lack of expertise at board level," said Jill Lane, the ministry's national health board director.
The Taxpayers' Union called for changes to the Official Information Act to cover groups such as the trust.
"Unlike government agencies, these non-profit groups are not required to comply with the act. This means that too often, taxpayer money disappears into a void," union executive director Jordan Williams said.
Prime Minister John Key said he had not received any advice on the trust.