Homeowners are being overcharged by up to £50,000 in a mortgage scandal involving some of Britain’s biggest banks and building societies.

Evidence drawn up by an independent financial auditor reveals a catalogue of mistakes made by Nationwide, Alliance & Leicester and Abbey that led to some customers being overcharged interest for up to 15 years.

The blunders centre on repayment mortgages – the most popular type – as their complexity makes it hard to spot mistakes.

Last night Jim Cousins, a Labour MP on the Treasury select committee, described the evidence as “extremely worrying” and called for random checks on mortgage providers to determine the extent of the problem.

Out of more than 30 mortgages reviewed by BankCheck, an auditing firm, the interest charged on monthly repayments was wrong in all the cases – and always to the customer’s detriment. The lender never lost out.

In one case, a farmer was overcharged £56,520 by Nationwide following two separate mistakes, but the building society, blaming human error, only refunded the money after BankCheck high-lighted the problems.

Trevor Hillen, a director of BankCheck, said: “On the law of averages, you would expect 50 per cent of mistakes to be in favour of the customer and 50 per cent in favour of the lender. However, we always see them in favour of the bank.”

Although the lenders insist the problems unearthed by Hillen’s firm are one-off errors, normally due to mistakes in keying in data, they adopt very different procedures to monitor their mortgage accounts.

While Alliance & Leicester claims it reviews accounts and data on an “ongoing” basis to ensure interest and repayment rates are correct, Nationwide and Abbey admitted they do not make routine checks after the initial mortgage offer is accepted.

As repayment mortgages require monthly payments that include some of the capital borrowed, they are more difficult to calculate than interest-only loans.

One case involved a 46-year-old businessman who took out a £15,000 mortgage with Alliance & Leicester in the 1980s and was quoted an 11.75 per cent rate. It should have been 11.25 per cent, and the society continued to overcharge by 0.5 per cent for 15 years.

Alliance & Leicester says the wrong figure was keyed in and has refunded £2,189.

The businessman said: “I think people have every right to be sceptical about banks and building societies.”

Terry McDowell, 52, an aero-space engineer from Ballyclare, Northern Ireland, was undercharged by Abbey for a £19,000 mortgage taken out in 1982.

The mistake only came to light in 2004 when McDowell received a statement telling him the bank had extended his 25-year mortgage by six years. When he queried this, the bank doubled the repayment figure overnight. BankCheck calculates he is out of pocket by up to £7,000.

Abbey insists McDowell misunderstood the terms of the agreement, a view shared by the Financial Ombudsman Service when it reviewed the case. “Checks are built into our mortgage processes. We are confident that this process is robust,” said Abbey.

Alliance & Leicester claimed new computer systems meant the type of mistakes uncovered in the audit could not reoccur.

Nationwide said mistakes occurred in a “minority” of cases. “We are confident in the integrity and accuracy of our systems.”