Hospitals are losing income because they are failing to get to grips with the Department of Health's choose and book system.
Commissioners and clinicians are complaining progress is being hindered by software glitches, a lack of appointment slots and GP apathy.
Commissioners say hospitals that do not make the most of the system will see patients deserting them for trusts and private providers that have largely embraced it.
They fear continued problems could further damage the credibility of choose and book, which is popular with patients when it works. Last summer a senior DH official criticised "significant numbers" of hospital trusts for holding appointments back from the system.
East and North Hertfordshire primary care trust chair Pam Handley said her PCT had been working with East and North Hertfordshire hospital trust to boost appointment availability. The trust had promised a 10 per cent month on month improvement, which has not yet been delivered.
Two trusts in the PCT's patch had also cut online referrals drastically for several months because software upgrades had to "bed down".
"Every time we think we've cracked it, something else comes up," she said.
She said the combined problems risked choose and book being viewed "cynically" by patients.
"Trusts that don't [make it work] will lose income. Private providers are much cuter on this - we've seen a shift to private provision because they do get their information up [on the choose and book site]."
Hull PCT chief executive Chris Long said: "Choose and book is something worth protecting - there are plenty of people who are opposed to it and I'd be really worried about anything which gave them ammunition to discredit what is a very good system for patients."
A letter from Tower Hamlets PCT to local GPs informed them of one case in which 442 patients waited on average six weeks longer than the 13-week national standard after more than 2,000 telephone bookings were left unprocessed on a spreadsheet at Bart's and the London trust.
The trust said the patients were delayed because of "inadequate management systems" in its central appointment office but an audit found no clinical harm had come to any patient as a result.