Current NHS data on GP consultations do not differentiate between patients experiencing long waits to be seen and those booking in advance or waiting for a specific doctor.
Dr Richard Vautrey said this was 'unhelpful' for identifying practices with genuine workload problems and made it difficult to know which types of consultations patients were struggling to access.
Unclear data could also lead to the government setting ‘unhelpful or damaging access targets’ that would pile additional pressure onto an already overburdened workforce, he warned.
The warning comes just months after Boris Johnson told MPs in his first speech as prime minister that he had 'asked officials to provide policy proposals for drastically reducing waiting times for GP appointments'.
Recent data from NHS Digital suggested that around one in six appointments took place more than two weeks after they were booked in the last year - although the proportion of these booked ahead deliberately is unknown. Almost seven in 10 GP appointments were delivered within a week or less.
Speaking at the Best Practice conference in Birmingham, Dr Vautrey said the way practices collected patient consultation data was not standardised, making it more difficult to gather and interpret data.
To gain a truer representation of access trends, the Leeds GP said practices should be helped to collect more detailed information about consultations.
‘In the last year or two, the NHS has started to collect regular appointment data. But the problem is that it’s not very specific. [It doesn't show] whether people are choosing to book ahead, or whether they simply can’t get an appointment and that’s why they don’t receive an appointment for two or three weeks.
‘GPs should be helped to be more specific about how they record appointment data. [This will show] whether practices are really under pressure and in what areas they are struggling, whether that’s face-to-face consultations, telephone consultations or home visits.’
With demand on general practice rising, Dr Vautrey said it was unsurprising that more patients were finding it difficult to secure an appointment.
Primary care access targets were scrapped by the government in 2010 to help clinicians prioritise patients and create savings. Dr Vautrey warned against bringing these targets backed based on flawed data.
He said MPs were under huge pressure from constituents over access to GP appointments, but warned: 'We need to avoid the risk of unhelpful or damaging access targets that simply can’t be achieved with the workforce we’ve got.'
Dr Stephen Miller, clinical director of primary care technology at NHS Digital said: 'We have a statutory duty to continually improve the quality of the data we collect.
'As part of this, we are exploring how we might be able to introduce a standard for appointment categories across all GP systems, in collaboration with partner organisations, GP practices, system suppliers and other stakeholders.
'This work would aim to provide nationally consistent reporting of the prevalence of different appointment types, without adding to the administrative burden of GPs or other practice staff.
'At all stages, changes are driven by and informed by the user needs of our stakeholders, most importantly, GP practices.'