Dr McGee dismissed every ground the minister and ministry used to support their stands, saying they should not have refused to release various documents concerning plans for the national collection of newborn baby bloodspot cards.
The documents were eventually released to the newspaper, months later than originally sought and around the same time decisions on the future management of the two million blood spot cards in the national Newborn Metabolic Screening Programme were made public last September.
At that stage, the Ombudsmen's office had not been able to complete its investigation.
The newspaper decided to persevere with the complaints because of concerns legitimate Official Information Act ( OIA) requests could be delayed apparently to suit political agendas, with those doing so taking the gamble that if documents were eventually released, breaches of the OIA would be ignored.
The information sought included consultation documents on the proposed protocols for the management of the blood spot cards (sometimes called Guthrie cards, and used to screen babies for a variety of metabolic disorders).
These were sent to selected groups for comment early last year and requested by the newspaper after that.
Among the grounds used by the Ministry of Health to refuse the ODT this information was that the documents were confidential and making them available would be likely to prejudice the supply of similar information or to damage the public interest.
"I cannot see how the ministry can owe an obligation of confidence in regard to consultation documents that it created itself.
It is clear that the ministry can choose to release, and did eventually release, the consultation documents at any time without regard to any obligation of confidence," Dr McGee said.
He added the consultation documents were at a final stage when released for consultation.
It was hard to see how release of the consultation documents to the newspaper, when the ministry had already carried out targeted consultation, would impact on the ability of the ministry to provide future free and frank opinions to the extent that it would prejudice the effective conduct of public affairs, Dr McGee said.
He also did not accept that the submissions on the consultation documents should have been withheld, pointing out submitters had been advised about the likelihood their submissions might be made public under the OIA.
"None indicated that they were opposed to this, and none indicated that they would like their personal information removed ... In these circumstances, it is inconceivable that release of documents that the authors were aware may be released would inhibit the free and frank expression of opinion in future submissions."
Disclosure of submissions could not pre-empt or prejudice the ability to consider later advice that may in part be based on the submissions, he said.
Dr McGee took issue with the ministry's use of the ground to refuse a request on the basis that information requested is or will soon be publicly available.
He pointed out that while the information sought by the ODT had been eventually made available to the newspaper, it had not been made publicly available.
Dr McGee also found Minister of Health Tony Ryall should not have refused to release the July 2010 Cabinet paper which informed the decision to keep the cards permanently.
This decision was first made public by the ODT in April last year. It followed considerable controversy, mostly behind closed doors, on issues around consent and possible future use of the cards and whether the collection should be kept permanently.
Mr Ryall advised in May last year he had withheld this document because further advice was "under active consideration".
However, Dr McGee found the withheld paper did not disclose any matters which remained under Cabinet consideration.
The paper had advised about whether the cards should be retained permanently and that decision had already been made - in July 2010.
At that time, the Cabinet Social Policy Committee invited the minister to report back on the new policy and governance arrangements. This was done in August last year.
At the time of the response to the newspaper's request, the committee had not considered the new policy and governance arrangements, but Mr McGee said releasing the earlier Cabinet paper would not have prejudiced the ability of the minister or the Cabinet to consider the subsequent August 2011 paper.
Dr McGee made no recommendations on the complaints, as the information sought had eventually been released to the newspaper.
• The Office of the Ombudsmen is yet to report on the outcome of the ODT's requested review of the process used by the Ministry of Health in developing protocols for the bloodspot cards.