GPs need to be assured that they will be commissioned to provide a wide range of services or that the PCT will leave space in the surgery before investing or taking a loan to expand, it says.
Dr Hamish Meldrum, the GPC chairman, was responding to assertions by health secretary Patricia Hewitt that there was no crisis over GP premises funding.
Dr Meldrum said premises was a huge issue, which the GPC was in the process of reviewing. Based on feedback so far 'there is considerable anxiety about the state of premises in general practice,' he added.
Ms Hewitt said last week that GP premises was not a crisis issue requiring the government to provide extra funding.
She said that GPs should not be asking for more money, but saying: 'Here's this rapidly growing budget. How can we use it?
'Capital funding for premises is not a big issue in most areas,' she added. 'The truth is there's big capital investment, not just in acute hospitals, but in primary care, especially LIFT.
'The real issue is revenue funding.'
Ms Hewitt called on GPs to follow GPs in Dudley PCT in the West Midlands where the health community had reconfigured services and saved money by targeting frequent A&E attenders.
Dr Meldrum agreed that capital funding was not necessarily the major issue.
'But when it comes to guarantees for future revenue, practices need assurances for the long term - 15 to 20 years. If they have that, capital is not such a problem,' he added.
GPC negotiator Dr Peter Holden said the premises issue could derail the government's reform programme, including its White Paper plans and practice-based commissioning.
A DoH claim that 3,000 new practices had been built or refurbished since 1997 was 'almost a complete work of fiction' that re-used old examples, he said.
According to Dr Holden, most premises money was not ring-fenced and had been used by PCTs to bolster MPIG.
'In reality there has been no money for premises for years outside LIFT schemes,' he said.
GPC member and chief executive of Wessex LMCs Dr Nigel Watson agreed, saying many GPs were unable to access LIFT money.
'We have lots of practices that have premises that are not fit for purpose,' he said. 'They can't provide GP services, let alone transferred work from secondary care.
'LIFT funding is not available everywhere. Bankrupt PCTs are hardly going to invest in GP premises.'
Specialist GP accountant Bob Senior, from Tenon Medical Services, said: 'We are not seeing capital investment reaching the majority of practices.
'While the government may be addressing some particularly high-need situations through LIFT, most practices are struggling to obtain any help with investment.'