The warning came after the government said the funding should be used to provide specialist care services in the community and to link GPs with job centres.
A total of £1bn spent over four years will 'pay for the modern premises and technology that will give patients access to advanced care, such as chemotherapy and dialysis, in their local communities', the Treasury announced.
It added: 'These new primary care facilities will also be encouraged to join up closely with local job centres, social services and other community services, to ensure the NHS is also supporting people back into the labour market.'
A £200m 'transformation fund' in 2015/16 will 'deliver the first year of the Five Year Forward View', NHS England's plan for the health service. 'The fund will kick-start work needed to develop new ways of caring for patients, to improve the integration of GPs, community services and hospitals', the Treasury said.
The Forward View set out new models to reconfigure GP services alongside community or secondary care. NHS England will make decisions on how the money is spent.
GPC executive lead on premises Dr Brian Balmer welcomed the chancellor's announcement, but said now the nitty gritty of working out how money would be delivered must begin (see box below).
Dr Balmer said the funding must not be 'diverted away to other pet projects of the health secretary'. He said a speech by Jeremy Hunt suggested the government was moving away from spending the money on GP premises.
'It was noticeable that the term GP infrastructure seemed to apply to a much broader range of issues than premises, which had appeared to be the main focus just 24 hours earlier,' Dr Balmer said.
A focused strategy emphasising GP premises should be agreed quickly, he said. 'We need holders of the pursestrings to talk to all interested groups across England, so upgrades to premises actually reflect what each GP practice needs for its patients.'
The chancellor announced a total of about £3bn in NHS funding; £1bn will come from a levy on banks, £1.3bn from underspends in other departments, and £700m from DH back office spending.
About £237m will be made available for Scotland, Wales and Northern Ireland.
RCGP chairwoman Dr Maureen Baker welcomed the 'urgent injection of investment', but warned it should not be 'siphoned off to pay for other urgent priorities'.