The annual allowance is the limit to the total amount of contributions that a saver can pay into their defined contribution pension and claim tax relief on and is currently capped at £40,000.
Amounts exceeding the limit will be taxed at the saver's marginal rate of income tax.
But in April last year the government put in place a tapered annual allowance for savers earning more than £150,000.
This means there is a reduction in the annual allowance of £1 for every £2 that the adjusted income exceeds £150,000, up to a maximum reduction of £30,000.
According to new data from the Office for National Statistics (ONS), there are 131,000 employees earning more than £150,000 – 85 per cent are men, almost 60 per cent are based in London and 35 per cent work in financial services.
However, the complex rules mean that more people are impacted, as income from other sources like dividends, property and interest are also included, as well employer pension contributions, Hargreaves Lansdown warned, meaning 364,000 savers are potentially affected.
As a consequence of including several types of income, "it is absolutely impossible for an employer to know an employee's total income in advance of the end of the tax year and provide assistance; it is also very challenging for many individuals to know their total income," Nathan Long, senior pension analyst at Hargreaves Lansdown, said.
This will mean that individuals won’t know for sure what their annual allowance for the year is, Mr Long added.
According to Mr Long "the rules for higher earners wanting to pay into pensions are now fiendishly complex".
He said: "We expect the last-minute rush to file tax returns will leave many realising they face a tax bill courtesy of the latest raid on pensions.
"Employers in London in particular look set to be inundated with queries from higher earners who are facing up to a tax charge."
According to the ONS data, upwards of 11 million tax returns are due to be completed, with 18 per cent expected to be filed in January – the deadline for filing tax returns for 2016 to 2017 - based on previous history.
Mr Long said: "This huge disruption based on a small number of people really highlights the need for wider reform to pension taxation, as opposed to the continued salami slicing we have seen in the past.
"Governments and regulators must realise that while these rules impact on higher earners only, the trickle-down complexity to all pension savers is a very high price to pay."
Pension provider Prudential has issued a similar warning, saying that the current rules around the tapered annual allowance could lead to people breaching their tax relief limits if they don't use an adviser.
However, for those who have overpaid, all may not be lost, said Mr Long as it is possible to carry forward unused contributions from previous tax years dating back to 2013 to 2014 and use them in the current year.
To benefit from this rule, the individual needed to be a member of a UK registered pension scheme in the years where he is bringing forward unused relief.
The amount the saver can carry forward depends on how much unused annual allowance he has in each of the last three tax years.
The individual must include their own pension contributions, any made by the employer and the value of any benefits built up in a defined benefit scheme.
maria.espadinha@ft.com
