Four of the city's five PCTs were the only ones in England to miss a June target for Choose and Book worth around £6,000 per GP practice.
The target - to have 30 per cent of GPs registered to be able to use Choose and Book - slipped because of technical problems with connecting to a directory of services for Leeds Teaching Hospital Trust.
Leeds LMC chairman Dr Richard Vautrey said most PCTs invested the money in improving IT equipment at GP practices, and without this investment, Leeds GPs would struggle to take on new IT initiatives.
'All our PCTs are struggling financially and this would have been a welcome boost for IT budgets at a time when we are starting to implement Choose and Book,' said Dr Vautrey. 'It is unfair if other areas have invested this money in practices and Leeds practices are unable to receive it.'
However, Dr Helen Alpin, professional executive committee chairwoman at East Leeds PCT, said the PCT missing out on the additional funds would not disadvantage practices signing up for the choice directed enhanced services.
She pledged that the PCT would make sure practices had the IT hardware they needed to meet targets.
'This was a small amount of extra funding and we missed out,' she said.
The four PCTs have lodged an appeal against the decision not to award them the payments.