The unauthorised release of a New Zealand journalist's phone records has claimed the head of the Parliamentary Service.

General manager Geoff Thorn resigned on Thursday morning, two days after Speaker David Carter admitted Fairfax reporter Andrea Vance's phone records were given to the inquiry into who leaked her a report into illegal spying by the NZ spy agency GCSB.

He had earlier said the phone records were not released, despite being requested by the inquiry.

In a statement on Tuesday, the inquiry's head, David Henry, said he did not ask for the phone records, and they were not looked at by his inquiry.

Mr Carter issued a statement on Thursday afternoon saying he has accepted Mr Thorn's resignation "with regret", and Friday will be his final day in the role.

Mr Carter said Mr Thorn had overseen a significant improvement in the Parliamentary Service's operations.

"However, both he and I acknowledge that the confidence in Parliamentary Service has been undermined by events in recent weeks, and as general manager he accepts responsibility for this."

Vance's phone records were released to the inquiry following an email to the Parliamentary Service from Prime Minister John Key's chief of staff Wayne Eagleson, sparking accusations of Mr Key's interference.

The inquiry previously prompted independent MP Peter Dunne's resignation as a minister after he refused to hand over his emails with Vance, a former News of the World reporter.

Mr Dunne denies being behind the leak of the GCSB report.

It has previously been revealed that the Parliamentary Service gave the inquiry Mr Dunne's email logs without his permission, and Vance's security swipe card data without her permission.

Mr Dunne on Thursday said he believes logs of his parliamentary cellphone were also given to the inquiry.

He says he gave permission for his landline phone logs to be released, but not his mobile phone records.