Patricia Hewitt, the health secretary, yesterday denied the government was responsible for a decision to withdraw a routine treatment from NHS patients which cured Tony Blair's irregular heartbeat in 2004. But her assurances were challenged by cardiologists, who insisted that a pricing bungle by the Department of Health was to blame and that hundreds of patients would suffer as a result.

The Guardian disclosed yesterday that Oxford Radcliffe NHS trust has removed about 50 patients with the same condition as the prime minister from its waiting list, in an attempt to balance the books. It will no longer perform cardiac catheter ablations - day surgery to restore the normal rhythms of the heart - unless the patient's condition is a lot more serious than his.

Consultants at the John Radcliffe could perform the operation for about £4,000, but under the government's new system of payment by results the trust received £2,007 for doing the work. So the trust lost about £2,000 on each patient.

Ms Hewitt said: "It's not at all clear to me why the costs at the Oxford Radcliffe of doing that particular procedure are so much higher than the average ... Gordon Brown has written a very, very big cheque for the NHS. But it is not a blank cheque."

But the Arrhythmia Alliance, a charity promoting better understanding of the condition, rejected her criticism of the Oxford consultants. Adam Fitzpatrick, its medical director and a Manchester cardiologist specialising in ablations, said a recent survey showed the average cost for a simple procedure was £4,500. More complex cases could cost up to £9,000.

"The tariffs set under payment by results were extremely low because of inadequate research into the cost profile. I doubt there was a heinous motive. It was probably just ignorance," he said.

Trudie Lobban, the alliance's founder trustee, said the Oxford decision was also influenced by pressure from the government to reduce maximum waiting times to six months by the end of December.

She said the target was particularly difficult to achieve in specialisms with a shortage of consultants. The ablation procedure was included in the national standards for heart disease for the first time in March and there were only 64 consultants in England able to perform it. But the government made no exceptions to the maximum waiting time. "Some of these patients cannot work - yet Tony Blair had the operation and he was back at work the next day, running the country. It is a scandal what they are doing. These poor people are being made scapegoats for the bureaucracy which goes on behind."

Ms Hewitt said she was proud of the six-month target and insisted it was not behind the decision.

Stephen Eeley, an Oxford university administrator who was dropped from the waiting list for an ablation, said he was being deprived of a simple operation that could prevent him constantly feeling breathless and tired. "To suffer what Mr Blair suffered and to have no recourse to anybody is extremely frustrating," he said. "It's very cynical that the Radcliffe hospital have chosen [to discontinue] this particular procedure, which I understand they do very well. It's a short-term fix to massage figures. This is not a life-threatening condition but it is a condition that massively reduces quality of life."

The Oxford trust said the decision to remove patients from the waiting list was taken by the local "priorities forum", including hospital consultants, GPs, pharmacists and public health specialists. "There is not a never-ending pot of money. Trusts need to balance their books," a spokeswoman said.

Evan Harris, Liberal Democrat MP for Oxford West and Abingdon, who blew the whistle on the decision, said: "Tony Blair was lucky to get his heart done before he imposed this NHS tariff nonsense on everyone else. Patricia Hewitt claims this was a local decision, but the six-month limit on waiting is national, the inadequate NHS tariff is national and the national standard for treating arrhythmias with ablation is national."