The doctor’s union branch in Scotland had polled 354 members and found the average tax bill due to annual allowance and lifetime allowance breaches was £18,500.
Some of the consultants, GPs, NHS staff and associate specialists polled had already received their bills while others were expecting them. A further 21 per cent were worried they could be receiving a large bill.
According to the survey the majority of doctors said they were concerned about the uncertainty surrounding their tax bills.
The GPs said the pension updates ran so far behind that they often have no idea about potential tax charges until it is too late.
Other doctors reported the system was so complicated it made it "difficult to make fully informed choices".
Concern about doctors' pensions has increased significantly since the introduction of the tapered annual allowance in 2016.
This gradually reduces the allowance for those on high incomes, meaning they are more likely to suffer an annual tax charge on contributions and a lifetime allowance tax charge on their benefits.
The tapered annual allowance means that for every £2 of adjusted income above £150,000 a year, £1 of annual allowance will be lost.
It emerged in December that the number of members leaving the NHS Pension Scheme was five times higher than that seen by other public pension funds.
The BMA survey seemed to back this up as it showed that across all branches of the profession, more than half of doctors have either already reduced their workload, or are planning to, in order to avoid their income breaching the relevant pension taxation thresholds.
In total, 87.4 per cent of doctors believed this trend would have a significant, or very significant impact on NHS services, such as waiting lists and emergency care.
More than a quarter of doctors felt it may actually lead to services collapsing.
According to Simon Barker, chair of BMA Scotland’s consultant committee, it’s "hard to overstate the seriousness of this situation and its implications not just for consultants, but for NHS hospital services and our patients who rely on them".
He said: "Make no mistake – our consultant workforce is already stretched to its limit, with high levels of vacancies.
"Added to this we are now seeing doctors across the profession cutting down their work, due to a completely justified fear that they will be hit with huge pension tax bills that are extremely hard to foresee.
"In worst case scenarios, a substantial number of doctors are telling us they are going to retire or are at least contemplating it."