Accountants have accused the Government of seeking to raise hundreds of millions of pounds from the public in accidental overpayments in the new era of online returns, citing HMRC’s botched handling of a shift to digital tax filings as fresh evidence of the dangers.

The National Audit Office reported this week that staffing failures at HMRC have cost customers an extra £33.6m in wasted time and potentially resulted in up to three million people paying the wrong amount of tax.

The damning report comes at an awkward time for the Government since ministers are expecting a wholesale switch to digital tax records to raise an extra £610m from the public a year by 2021 while simultaneously slashing HMRC staff costs.

Some accountants suggest the digital switch plan, outlined by George Osborne in last year’s Autumn Statement, will amount to a “fat finger tax”, meaning the Treasury expects to benefit from over-payment mistakes by people filling out their forms online.

“Anything that moves to trying to cut out accountants will not make the system more accurate, it will make the system less accurate” said Cormac Marum of the accountancy firm Harwood Hutton.

“There’s got to be a significant risk that people do end up overpaying tax” said Aidan Sutton, a partner at PwC. “There’s a difference between filling out a tax return and sending it off at the end of the year and a website telling you ‘your balance is this’. A lot of people won’t have the expertise to challenge this number. It’s rare for HMRC to make errors in the taxpayer’s favour than in their favour”.

The Treasury insisted today that its costing were based on the assumption that the money would be raised by eliminating underpayments, rather than scooping up accidental overpayments.

“Suggestions that enabling businesses to handle their tax affairs online will lead to more errors and extra tax revenue are simply false” said a Treasury spokesperson.

But the latest NAO report highlights how “errors in online guidance” from HMRC could contribute to customer mistakes in both directions.

The official Government auditor checked 51 questions on the online HMRC self-assessment form and found supporting guidance was incorrect for three. “One created potential for a taxpayer to overpay £126,000 in tax. Another created potential to underpay £11,000 in tax. We do not know if any customers have gained or lost from the errors” it said.

Last Autumn Mr Osborne announced an 18 per cent real terms cut in HMRC’s day-to-day budget over five years combined with a £1.3bn investment in the agency’s digital capabilities.

“In the digital age we don’t need taxpayers to pay for paper processing, or 170 separate tax offices around the country” the Chancellor said.

”We’re going to build one of the most digitally advanced tax administrations in the world. So that every individual and every small business will have their own digital tax account by the end of the decade, in order to manage their tax online.”

But the NAO found HMRC’s attempts to reduce the number of customer service staff and transfer more resources into the automated tax processing had gone “badly wrong”, leaving phone lines undermanned at a time of high demand.

The NAO said the quality of service provided by HMRC for personal taxpayers “collapsed” in 2014-15 and the first seven months of 2015-16 when average call times to HMRC tripled.

According to the NAO the stock of outstanding discrepancies in tax records requiring investigation rose from 2.4 million in 2014 to 4.6 million in 2015 and that 3.2 million of these were high priority cases “carrying a risk that employees will have paid the wrong amount of tax”.

The NAO estimates the overall cost incurred by customers (in wasted time) who called the HMRC tax helpline increased from £63m in 2012-13 to £97m in 2015-16.

HMRC has said there was “no evidence” its poor service had impacted on its overall tax revenues, citing the findings of various focus group studies in which people said that they would not evade tax because of a poor customer service by the authorities.

The Office for Budget Responsibility has given a “high” uncertainty rating to the HMRC estimate in the Autumn Statement of the amount of money that will be made from moving to digital tax filing. This is estimated at £10m in 2018-19, rising to £300m in 2019-20 and £610m in 2020-21.

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Ruth Owen, HMRC’s Director General for Customer Services said in response to the NAO report that: “We recognise that early in 2015 we didn’t provide the standard of service that people are entitled to expect and we apologised at the time. We have since fully recovered and are now offering our best service levels in years.”

Between 2010-11 and 2014-15, HMRC cut staff in personal tax from 26,000 to 15,000. The total budget of HMRC in nominal terms is due to fall from £3.5bn in 2015-16 to just £3.1bn in 2019-20. Last Autumn HMRC said it expects the number of calls it receives a year to fall from 38 million to 15 million.