Nearly £3 million has been set aside by the Welsh Assembly annually since 2004/5 to improve GP surgeries, yet between £1.1million and £2.8 million was left unspent each year.
Only 13 of the 22 Local Health Boards (LHBs) have made successful bids to the fund, set up in 2004/5 to improve GP premises.
The Western Mail reported that as many as three quarters of practices in some LHBs are substandard or require investment.
The long-term cost of modernising GP practices in Wales is at least £100 million, said Welsh GPC chairman Dr David Bailey. The figure was £40 million in Newport alone.
Just half of the LHBs responded to a Freedom of Information Act request by the BMA to reveal the estimated cost of modernising their practices.
BMA figures also show that since 2004, the average number of new premises built in Wales is just one per LHB, compared with over four per PCT in England.
Dr Bailey said: ‘We've lost two or three years of funding. There are whole areas of south-east Wales where practices are getting more and more dilapidated.
‘Many of the buildings are not fit for purpose - they are old houses - and there isn't enough room for training facilities for registrars. We'd like to get on with shifting services into the community but there aren't any rooms.'
Dr Bailey believes the funds were held up by the LHB's slow, bureaucratic application process.
‘The money is not released until the LHB's premises strategies are approved. Five or six were nearly two years late handing in theirs. That's just incompetence.'
A spokesman for the Welsh Health and Social Services board said on larger projects, the money would not be released until all the work was complete.
‘We anticipate that all the money set aside for 2008/9 will be fully spent on improving GPs premises.
‘We expect that now LHBs have completed their primary care estate plans we will receive an increasing number of bids,' he said.
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