STPs 'present an opportunity to move care closer to home and moderate demand for hospital services', the King's Fund report says.
But it warns that plans to cut numbers of hospital beds are not credible 'unless investment is first made in services in the community', and that the ongoing NHS crisis could 'divert attention from work to transform care'.
The warning came as NHS Improvement said its latest findings on NHS trust finances showed that providers were 'experiencing one of the most challenging winters on record'. NHS trusts ended the third quarter of 2016/17 with a combined deficit of £886m.
NHS Improvement said severe pressure on hospitals had cut their income as many were forced to reduce planned care and focus on extra emergency work - GPonline reported on Monday that a fifth of hospital trusts in England had spent half of 2017 to date on one of the highest two alert levels possible.
The BMA warned that growing pressure on the NHS meant that STPs risked becoming a vehicle for cuts rather than transformation or improvement of services.
Writing for GPonline, RCGP chair Professor Helen Stokes-Lampard warned that STPs were prioritising hospitals over general practice, and urged the government to honour promises to invest in primary care.
King's Fund chief executive Professor Chris Ham said: 'It is not credible for the government to argue that it has backed the NHS’s own plan unless it is prepared to support changes to services outlined in STPs.
'Local plans must be considered on their merits, but where a convincing case for change has been made, ministers and local politicians should back NHS leaders in implementing essential and often long-overdue changes to services. A huge effort is needed make up lost ground by engaging with staff, patients and the public to explain the case for change and the benefits that will be delivered.’
BMA chair Dr Mark Porter said: 'The STP process could have offered a chance to deal with some of the growing problems the NHS is facing, such as unnecessary competition, expensive fragmentation, and buildings and equipment often unfit for purpose.
NHS risks collapse
'We already know that the vital funding needed to carry out these plans simply isn’t available. From the beginning, this process was rushed and carried out largely behind closed doors, by health and social care leaders trying to develop impossible plans for the future while struggling to keep the NHS from the brink of collapse.
'These plans are fast becoming completely unworkable and rather than transforming the health and social care system, have instead revealed a health service at breaking point - one that is unsustainable without urgent further investment, and with little capacity to ‘transform’ in any meaningful way other than by reducing the provision of services on a drastic scale. Improving patient care must be the number one priority for these plans. Given the scale of the savings required in each area, there is a real risk that these transformation plans will be used as a cover for delivering cuts, starving services of resource and patients of vital care.'
A DH spokeswoman said: 'The NHS has worked hard to manage its finances in a challenging period, and the hospital sector's financial position has now improved by £1.3bn compared to this time last year, with 44 fewer trusts in deficit.
'While a significant majority of hospitals are now reducing the cost of expensive agency staff, there is more to do to drive efficiencies.'
The spokeswoman said the government was 'investing an additional £10bn in the frontline'. The House of Commons health select committee, among others, has questioned the use of this figure, arguing the true figure the government will invest by 2020 is closer to £4.5bn.
On STPs, a government spokeswoman said: 'These NHS plans - developed by local doctors, hospitals and councils working together with the communities they serve - will help patients get better care by delivering the NHS's Five Year Forward View, transforming mental health provision, improving cancer care, and delivering better access to GPs.