Peers will scrutinise the Bill and consider potential amendments during a 'committee stage' starting on Tuesday, which is likely to continue into November.
The BMA said it was increasingly important to secure clarification on the Bill as the government continued to push ahead with the reforms.
It warned that the Bill could give the NHS Commissioning Board (NCB) ‘overly restrictive powers’ over clinical commissioning groups (CCGs).
It said it would seek amendments and firm assurances that there was a genuine devolution of power and CCGs were given sufficient freedom to commission services.
The government must also provide a ‘clearer narrative’ on how CCGs, clinical senates and networks, health and wellbeing boards and the NCB will interact, it added.
The BMA has also demanded amendments to the Bill to prevent conflicts of interest arising from plans to link financial incentives to the performance of CCGs.
An amendment tabled by Conservative peer Lord Mackay of Clashfern calling for the health secretary’s responsibility for the provision of the NHS to be made explicit in the Health Bill was welcomed by the BMA.
BMA chairman Dr Hamish Meldrum said there was still an opportunity for ‘significant changes’ to the Health Bill. He said: ‘We hope the Lords will agree with us and change the proposed legislation, limiting the damage this Bill could do to the NHS.
‘Because so much of the detail won’t appear on the face of the Bill and will instead be left to secondary legislation and guidance, it is essential to have firm assurances now about the government’s implementation plans.’
It comes as the Royal College of Physicians called on the government to amend the Health Bill to ensure that specialist doctors and nurses who sit on CCG boards do not have to be from outside the local area. It said CCGs will need local knowledge to make the best commissioning decisions.