The British Medical Association chair of council has declared a cautious victory on NHS reform at the union’s annual representative meeting.

Dr Hamish Meldrum said there had been an “unprecedented” change to the government’s original proposals, much of which the BMA had strongly opposed.

In March Dr Meldrum faced down calls from some members for the BMA to stop “engagement” with the government on the plans and to tell its members to stop cooperating with the changes.

He defeated those calls in a vote at a special representative meeting (SRM).

Speaking today at the ARM, Dr Meldrum said: “In my speech to the SRM I said, ‘What we have to decide today is how to move on from here, how we are most likely to achieve change’.

“Since the SRM the government has paused, listened and reflected. As a result we have the prospect – and I do emphasise the prospect – of a significantly different bill and one on a significantly different track to that which was originally proposed.

“Yes, specific clauses have been defeated in government bills before and whole policies have been thrown out, but it is unprecedented for a government to change its headline legislation so significantly and at such a late stage in the process,” he told the conference.

“Stranger still, we’ve just experienced an intense period of genuine engagement with government, which followed one of the worst examples of stonewalling in my long experience,” he added.

However, Dr Meldrum said the BMA was still examining the detail of the government’s amendments to the Health Bill.

There was “still much detail to be devilled out, still much else we want to change”, he told delegates. He highlighted the affected areas as education and training, public health and competition proposals.

He also highlighted opposition to the proposed quality premium, which would reward practices and commissioning groups based on their performance. The government has said the plan will be reviewed, but provision for the premium remains in the redrafted Health Bill.

Dr Meldrum attacked the government’s pensions proposals for doctors, which is set to be the next major battle for the union.

In relation to pensions, he said: “Let me make it absolutely clear; we will consider every possible, every legitimate action that can be taken to defend doctors’ pensions. However, in doing so we should not and must not do anything that will undermine that trust that our patients and public have in us.”