Taxpayers will be hit with higher penalties for late self-assessment returns and unpaid tax under a tough new regime set to be announced within weeks.

Revenue & Customs has been holding secret talks with the tax industry on ways the penalty regime can be used to plug the £3.6 billion hole in the public accounts. Insiders are expecting the chancellor to unveil the new rules in his pre-budget report next month or in early December.

They say that the Revenue will hike the £100 penalty for late returns, possibly to £250. Taxpayers who then find they do not owe any tax will no longer be able to reclaim the fine.

The taxman could also levy higher penalties on people who pay too little tax unwittingly — perhaps because they fail to keep proper records or take advice. In the worst cases, the Revenue has the power to fine up to 100 per cent of the unpaid tax. Someone who underpaid by £3,000 could end up paying as much as £6,000.

An insider who has been involved in the talks, but who wished to remain anonymous, said: “We are expecting a dramatic regime change, both in terms of how much people can be charged and when the penalties can be levied.”

Thousands of ordinary taxpayers with no intention of defrauding the Revenue but with complex tax affairs are expected to fall foul of the new rules.

Anita Monteith at the Institute of Chartered Accountants, which has also been involved in the talks, said: “The late-payment penalty is going up and we’re going to get a more harsh regime, without proper consultation. The government needs more money and one of the ways of getting it is through the penalty regime.

“We want taxpayers to have adequate protection in place so they have a right of appeal if something goes wrong.

“We are concerned that some vulnerable groups, including pensioners, will be forced to pay late-payment penalties even if they don’t owe any tax.”

Accountants say inspectors are already clamping down on ordinary taxpayers for minor errors in anticipation of the new regime. Mike Warburton of Grant Thornton said: “I have a client who underpaid tax through no fault of her own — her bank amalgamated two loan accounts — and the tax inspectors are arguing that she is negligent. They want to charge her 25 per cent of the unpaid tax, the same as David Mills.” Mills, a corporate lawyer and estranged husband of culture secretary Tessa Jowell, was fined only 25 per cent of his unpaid tax despite having five offshore sources of income and gains.

Tax inspectors hope the Revenue’s new powers will help to retrieve up to £1 billion in unpaid tax and also slash the number of people who miss the January 31 deadline for filing their self-assessment returns — now standing at 1m.

At present, inspectors have broad scope to cut penalties on unpaid tax to nothing depending on the gravity of the “offence” and whether taxpayers co-operate and offer full disclosure of their affairs. Accountants say that thousands of clients who make minor errors pay nothing under this system.

Under the new regime, though, the Revenue will narrow the scope to reduce penalties and tighten up the rules on who should suffer fines. A taxpayer who simply “fails to take reasonable care” with his or her affairs could fall foul of the penalty regime. This could include “not putting in place appropriate accounting systems or keeping proper records or retaining relevant documents”, not “seeking properly qualified advice” and “not seeking advice from HMRC [the Revenue] where it is available”, according to consultation documents seen by The Sunday Times.