In his closing remarks he emphasised "the concern I have in hindsight about the way the inquiry went about its business.
"Direct approaches to third-tier staff and the service's contractor, in my view, compromised the service's position and my position as the holder of sensitive information on behalf of members.
"During the process I became concerned about the lack of formality or clarity about the inquiry's status and role. In hindsight I should have contacted Mr Henry directly and expressed my concern about the way the inquiry was going about its work. But I did not do so."
However, Mr Thorn told the committee he believed he was justified in releasing Ms Vance's swipe card records to the inquiry.
Earlier as Mr Henry faced the committee, Ms Collins openly criticised the inquiry, saying it was "chilling" to discover it had treated the privacy of ministers' and staff information in a "contemptuous way".
She asked why he had thought ministers had given permission for their records to be handed over, and he said he had assumed it had been authorised.
Later in the House when asked about Ms Collins' comments by Labour Deputy Leader Grant Robertson, Mr Key said that as Prime Minister "I put out terms of reference, and if any minister didn't like them they were free to complain about them."
Meanwhile, under questioning from Maori Party Co-leader Tariana Turia Mr Henry said he did not believe it was his job to find out whether he had authority to obtain various records. He left that to Parliamentary Service.
"I had reasonable grounds to expect that Parliamentary Service knew what they were doing."
The inquiry was set up by GCSB head Ian Fletcher and the head of the Department of Prime Minister and Cabinet, Andrew Kibblewhite.
United Future leader Peter Dunne was the chief suspect of the media leak and, after he refused to co-operate with the inquiry, he was forced to resign.
Mr Henry said at no time did the inquiry request the phone records of Ms Vance, a Fairfax reporter, although he did ask for the swipe card records in and out of Parliament of her and Mr Dunne relating to the time he believed the report had been leaked.
Police Minister Anne Tolley told Mr Henry she was surprised that he did not seek the advice of Speaker David Carter to clarify rules about parliamentary privilege.
"With 20-20 hindsight that might have been a wise thing to do," Mr Henry said, but he had assumed that Parliamentary Service, which reported to the Speaker, knew the rules.
Ms Vance's phone records were sent to the inquiry by Parliamentary Service but were not accessed.
The records of ministers and staff were sent on the understanding that the Prime Minister expected his ministers to comply with the leak inquiry. His chief of staff Wayne Eagleson wrote to all ministers' offices to set out that expectation.
Act Leader John Banks suggested during his line of questioning that the Henry inquiry had "trampled on the rights and freedoms of Members of Parliament and the fourth estate in a very cavalier manner."
Mr Banks also said it had been unfortunate and very unfair that Mr Thorn had lost his job as a result of the inquiry.
Under questioning, Mr Eagleson said if there were a repeat situation, he would approach individual ministers with a piece of paper to ask their permission to release their records.
Mr Kibblewhite said from the outset of commissioning the inquiry, it had never been anticipated that it would involve a journalist.
The terms of reference made it clear that the subjects of the inquiry were those people, including himself and ministers, who had been given an advance copy of Rebecca Kitteridge's report on whether the GCSB spy agency operated within the law.
Under questioning from Labour's David Parker, Mr Kibblewhite refused to state that a journalist's access records to Parliament should never be used in an inquiry.
If there were material matters of security involved, there could be circumstances in which it was appropriate to hand over a journalist's records.
He would not be drawn on whether that should relate only to physical security.
