The King's Fund report, Patient Choice: How Patients Choose And How Providers Respond, outlines concerns about the system.
It found that GPs still 'strongly criticise' its suitability for arranging appointments for treatment.
GPs were concerned about the system's technical shortcomings as well as the inability to refer to a named consultant and lack of directly bookable appointment slots.
The report said: 'If Choose and Book is to be used more widely, continued improvements will be needed in the systems and training in its functionality, especially if local incentives are dropped.'
The King's Fund looked at how patients who need a referral to a specialist are exercising their right to choose a provider.
The study found that patients living in non-urban areas were more likely than those in urban areas to be offered a choice and were more likely to choose to travel beyond their local provider.
The King's Fund also found that older patients, those from mixed or non-white backgrounds and those with no qualifications were more likely than other patients to think having a choice was important.
The study showed that just 4 per cent of patients consulted the NHS Choices website, with most preferring to rely on their own experience or the advice of their GP.
The King's Fund said that there remains 'some resistance' among GPs to offering choice routinely to all patients, regardless of circumstance.
Although GPs maintain that they always offered choice to their patients, only 49 per cent of patients recall being offered, the study found.
Anna Dixon, director of policy at The King's Fund and the report's lead author, said: 'While it is still early days, we are some way from realising the vision of choice acting as a lever to improve quality, with informed patients choosing the highest performing providers in a competitive market.'