At the BMA's annual representative meeting in Brighton last week, Andrew Lansley confirmed for the first time that not all commissioning would be controlled by consortia.
'General practice should see itself at the heart of delivering quality for patients,' he added.
The remarks brought a mixed response from GP leaders.
Deputy GPC chairman Dr Richard Vautrey said small scale commissioning could widen variation in services.
'If you had a patient needing expensive treatment then this will have a massive impact on budgets,' he added. But he admitted there were 'potential benefits' for practices.
NAPC president Dr James Kingsland welcomed the view that a 'one size fits all' commissioning model 'does not work'.
'There are some things at a smaller level that will be achieved very quickly, such as a physiotherapy unit attached to a practice,' he said. 'But a major redesign of services will have to be done at scale.'
Setting budgets at consortium level could speed up the introduction of commissioning, he added. 'Ideally, budgets could be set at practice level and aggregated up,' he said. 'But this might take too long.'
The Treasury told GP it was 'working closely' with the DoH on a White Paper expected to set out GP commissioning plans.
The document was expected in early July, but had yet to appear as GP went to press, amid speculation that it had been put on hold after senior NHS managers and the Treasury warned the scheme could put NHS finances at risk.
GPC chairman Dr Laurence Buckman said GPs were no more likely to overspend than managers. 'Claims like this are absolute nonsense,' he said. 'It's scaremongering.'
Dr Kingsland said practices may have to agree 'joint accountability arrangements' that incorporate a financial risk to prevent overspends.
He said: 'For some it's thinking the unthinkable; but we have to think like that if the NHS is going to survive.'
Meanwhile, the first three of around 150 NICE 'quality standards' that GP commissioners must meet were released last week, covering stroke, dementia and VTE.