HMRC has admitted that the site was giving incorrect figures, and has apologised for the error.
Under current rules, for most taxpayers, pension contributions of up to £40,000 per year qualify for tax relief.
But since 2016/17, higher earners have faced a reduced allowance, which can fall to as little as £10,000 per year for those on the highest incomes.
The impact of this change is reduced by the ability of taxpayers to ‘carry forward’ unused annual allowances from up to three years earlier.
But the HMRC website (https://www.tax.service.gov.uk/paac) was getting its sums wrong in some cases for both 2017/18 and 2018/19.
This could have led to individuals wrongly believing they should stop saving into a pension because they have exceeded their annual limit.
One Royal London customer, who used the site, was told that he was limited to £10,000 in pension contributions for 2018/19, when the correct figure was around £35,000.
HMRC admitted that the website was incorrect and have taken it down while work is in progress to update it.
When Royal London raised the issue with HMRC on Monday, it told the company: “We are aware that since 6 April 2018 the Annual Allowance calculator is showing less annual allowance than is due for the year 2017-18 onwards, and we apologise to customers for this.
“We’re working to fix this issue as soon as possible.”
Royal London’s director of policy, Steve Webb, called for “urgent action.”
He said: “It is totally unacceptable for an official government website to continue to operate when it contains blunders of this sort."
An HMRC spokesperson told Financial Planning Today: “We are sorry that the calculator isn’t working as it should in some cases.
"The calculator is no longer available as it is being updated.”
*Editor's note: This story was updated at 12.24pm after HMRC confirmed the site had been taken down to be corrected.