The government has vetoed the publication of a risk register on the implementation of its NHS reforms, which it had been ordered to publish by an independent tribunal.

The Department of Health’s decision to use the veto follows its battle to resist publication of the Transition Risk Register, which was requested under the Freedom of Information Act in November 2010 by then shadow health secretary John Healey.

In March an information tribunal rejected the DH’s appeal against the Information Commissioner’s ruling that the register should be published.

Instead of appealing again, health secretary Andrew Lansley has taken the rare step of using its power under the act to veto the request.

He has made the decision despite the leaking of a version of the Transition Risk Register later in March.

The ministerial veto has been used on three previous occasions - once when disclosure of Cabinet minutes on Iraq was ordered, and twice in relation to minutes of the Cabinet sub-committee on devolution.

A DH statement today said Mr Lansley had consulted the Cabinet and made the decision because it was an “exceptional case where there is a fundamental disagreement on where the public interest lies”. It said a further appeal tribunal would “focus on points of law arising out of the [previous tribunal] rather than the balance of the public interest”.

The statement reiterated the government’s position. It said: “Ministers and officials should be able to deliberate sensitive policy formulation, in expectation that their views are not published at a time when it would prejudice the development and delivery of policies. If such risk registers were regularly disclosed, it is likely their form and content would change, and they would no longer be the effective internal management tools they are intended to be.”

DH permanent secretary Una O’Brien and former cabinet secretary Lord Gus O’Donnell both made this argument determinedly at the tribunal hearing on the risk register’s release.

Mr Lansley said in a statement: “This is not a step I have taken lightly. I am a firm believer in greater transparency and this government and this department have done far more than our predecessors in publishing information about the performance and results of our policies.

“But there also needs to be safe space where officials are able to give ministers full and frank advice in developing policies and programmes.”

Alongside the announcement the DH has published a list of the issues which it says were covered by the register, and the “mitigating actions” which have taken place and which will take place in future.

A spokesman for the Information Commissioner’s Office said: “We will need to study the secretary of state’s statement of reasons for imposing the ministerial veto in this case. These must, under the criteria established by the government, be ‘exceptional’. We will present the commissioner’s formal report on the matter to Parliament next week.”

John Healey, who is no longer in the shadow cabinet, said in a statement: “This is a desperate act which will backfire badly. It is an admission of defeat on the legal arguments for public release.

“It is totally over the top to place NHS changes on the same footing as preparations for the Iraq war… The government has lost twice in law, yet still won’t accept that patients and NHS staff have the right to know the risks ministers are running with the biggest-ever NHS reorganisation.”