Speaking to GPonline, the RCGP chair said that the college supported greater integration in principle - even to the extent of pooling budgets across primary and secondary care within local areas or regions.
But he warned that although in some areas GPs' voice within local health systems was well established, in parts of the country dominated by powerful hospitals integration plans would not work.
In these areas in particular, NHS reform plans set out in a government white paper last month could lead to a reduction in funding for general practice - rather than the increased share of the health service budget the college and others have called for, Professor Marshall said.
As an academic who had studied integration over many years, the RCGP chair said he was well aware that there had been a string of policy initiatives that aimed to deliver integration over recent decades - and that 'none of them have worked very well'.
'I'm not expecting this to be easy territory in any way,' he said. 'But there's plenty of evidence that when you do have a well integrated system...you deliver better quality care at lower cost. We know that from international exemplars of good practice. So it's the right direction of travel.'
However, maintaining a strong voice for general practice within a re-shaped NHS landscape was crucial, he argued.
'That's where the issue around CCGs comes in. Whatever you think of their effectiveness over the last eight years, CCGs - because they've held budgets - have had a lot of influence on the way the systems work,' he said
'If CCGs are disestablished in the way that NHS England would like - and I understand why they might want that - the risk is that there won't be any force behind the GP voice, there won't be any incentives in the system to listen to GPs, and that's a concern.'
Professor Marshall said that integrated care systems with general practice and primary care as their foundation 'are the ones that work' - while those seeking to drive integration from hospitals 'don't work'.
'That's where my biggest concern lies - that general practice needs to have a very significant voice, a leadership voice, I'd say, in integrated care organisations, or integrated care systems.
'I am confident that in some parts of the country, the GP voice is sufficiently well established, relationships with hospital colleagues are sufficiently good for that to happen.
Integrated care systems
'But there are many other parts of the country where there hasn't been sufficient time to develop that collective GP voice, where there possibly isn't one, and where hospitals are very powerful - particularly in areas like cities where there are big teaching hospitals - where integrated care initiatives simply won't work, because they're driven by the hospitals rather than by general practice.'
In areas such as these, the RCGP chair warned - although pooled budgets in principle were 'exactly the right thing to do' to root out the 'dysfunction' that funding locked up in separate silos can create in health systems - funding could be sucked out of primary care.
'If you've got an integrated care system that doesn't work well, if the power is with the hospitals, the hospitals will demand more money and general practice will be starved and that would be a disaster,' Professor Marshall said.
In a speech at a virtual RCGP conference earlier this year, Professor Marshall argued that the share of NHS funding allocated to primary care - currently around 9% - should double, to bring the UK in line with some of the best-performing integrated care systems in the world.