GPs say that hospitals in areas including Bristol and London are refusing to release appointments more than a few weeks ahead, to ensure they meet waiting time targets.
Dr Chaand Nagpaul, a GPC member and a GP in north London, said some hospitals had even left the choice menu in order to prevent referrals.
'The real problem is not Choose and Book, but the hastily implemented and punitive 18-week target,' he said.
However, Dr Stephen Miller, medical director of Choose and Book, said hospitals cannot manipulate waiting times in this way.
If no convenient slots are available, the appointments line will instead send the referral by email.
'So it's not actually of any advantage to acute trusts not to put enough appointments on to the system,' he added.
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