BMA leaders condemned the situation as 'unacceptable' in a letter to NHS England chief executive Sir Simon Stevens, warning that thousands of GPs were at risk of ' an unfair and unreasonable financial impact'.
The letter also demands clarity over how the NHS England chief's promise to protect doctors from pension tax bills relating to the current financial year will extend to general practice.
Of 42,451 active records for GPs held by the NHS Business Services Authority (NHSBSA) - which administers NHS pensions - just 11,232 (26%) have been updated to the end of the 2017/18 financial year.
The figures came in a freedom of information response from NHS BSA to financial services company Quilter last month.
In a letter to Mr Stevens, BMA GP committee chair Dr Richard Vautrey said the figure was 'simply unacceptable'.
The GPC chair wrote: 'If the delays alone were not enough cause for concern, the situation is being further exacerbated by current pension taxation policies and their management. As you know the BMA, is more widely calling for tax reform to address the punitive annual allowance and taper policies.
'However, GPs are specifically impacted due to the delay in receiving pension statements, and in many cases not receiving them at all. It is leaving the majority of GPs without the relevant information to be able to make an assessment as to whether or not they are likely to face an annual allowance charge in any given year.'
Thousands of GPs have been forced to reduce their working hours or turn down extra shifts to avoid punitive pension tax bills that can leave doctors paying more in tax than they received for additional work.
Dr Vautrey also hit out at the continuing lack of clarity for GPs about how they would benefit from a promise made in November by NHS England that doctors caught in the pension tax trap could 'immediately' return to work because the health service would foot the bill for any tax penalties incurred for 2019/20.
A spokesperson for Capita, which runs Primary Care Support England (PCSE), said: 'PCSE is working closely with NHS BSA and other partners to improve the clarity around pensions for GPs.
'Currently pensions forms can sometimes be filled in incorrectly or with data missing. PCSE will always work with GPs to correct these issues and help ensure their records are complete. Last year we launched an amnesty with NHS England that allowed GPs to submit missing certificates from their pensions records going back 15 years.
'This was a successful project and over 40,000 certificates were provided by GPs to bring their records up to date. This year PCSE will launch a new service enabling GPs to submit their pensions certificates online. This will make the process more efficient, give GPs additional time to gather missing information and greater assurance that they have submitted all the required details by the deadline.'