Landlords are being forced to pay tax twice on the same gains and risk overpaying by hundreds or even thousands of pounds.

As of April 2020 anyone who sells a second home must pay any capital gains tax due on profits within 30 days. The rate of CGT paid depends on how much a taxpayer earns overall in a year. But HM Revenue & Customs' new system does not match up with annual tax returns.

This means landlords must make their best guess of what their tax bills will be, risk overpaying and seek a refund months later if necessary.

Chris Etherington of RSM, the accountancy firm, said the new arrangement was “not fit for purpose”.

“Lots of landlords have been without income for a long time during the pandemic and many do not know whether they will be lower or higher-rate taxpayers. If they end up overpaying HMRC is benefiting from sitting on that money while people who are struggling are left out of pocket,” he said.

As an example, someone who earned £60,000 last year and made a gain of £40,000 on a property sale this year would pay the highest rate of tax at 28pc, meaning a tax bill of £7,756 after the £12,300 allowance was taken into account. This must now be paid within 30 days of sale.

But if their income suffered because of the pandemic and turned out at the end of the year to be £32,000, it would mean they should actually have paid at a rate of 18pc – £1,750 less. Regardless, they must still pay their income tax bill for the year, on top of the already overpaid CGT, and then apply for a refund later.

Under the old system landlords held on to their cash until the end of the year, when their overall tax bills would be calculated at the same time and “netted off”. Mr Etherington said: “If nothing else, this creates unnecessary duplication of work.”

The Institute of Chartered Accountants said the system was “incredibly inefficient” for both HMRC and taxpayers. It is in discussions with the tax authority to find a better solution. It said the new 30-day window rules had been poorly publicised and the online system had produced incorrect tax bills because of technical flaws.

Some 16,000 landlords missed the short filing window last year, this newspaper disclosed last month, and thousands were issued with fines.

HMRC said no one would face late filing penalties this time if they were late because of glitches in the system, which it said had now been fixed. It apologised to anyone affected. A spokesman said: “We keep all our services under review and welcome views from tax professionals on making it as easy as possible for customers to get their tax right.”

The new regime is expected to boost tax revenues by £1.2bn by 2023.