Customers shortchanged by some of Britain’s biggest banks could lose out on tens of thousands of pounds in compensation as an unexpected consequence of the Office of Fair Trading’s (OFT) test case against penalty charges.

The OFT announced last month that it is taking the banks to court in an attempt to prove unauthorised overdraft charges are unfair. But bank-charge campaigners warn that even if a judge decides in their favour, thousands could lose out.

Most at risk are those who recently received an offer of a refund that falls short of what they expected. High-street banks have been forced to pay back millions of pounds in unfair overdraft fees in the past year, but some banks have been trying to fob off customers who complain with offers substantially lower than the sums claimed.

An e-mail leaked to The Sunday Times by an insider reveals that Halifax has been offering just half the sum requested. Lloyds TSB and Abbey also use this strategy, according to Conkers, a claims specialist.

You can turn down a partial offer and pursue your bank for the full sum. But the test case means if you reject what is on the table you could have to wait years for a bigger payout. The Financial Services Authority (FSA) has allowed banks to shelve complaints until the test case is resolved, which consumer groups warn could take up to three years. If the banks win the case there is even a danger that you may not get anything back at all.

Offers that have already been made have to be honoured. But savers who accept a payout are being told this will prevent them making any further claims, even if the banks lose the court action.

Halifax pays refunds directly into bank accounts and assumes an offer has been accepted if the funds are not returned in three months.

The e-mail seen by The Sunday Times said: “Assuming we lose the court case we would reject a further complaint as they have settled in full.”

Nicola and Clive Nicolello, from Fleck-ney, near Leicester, have been trying to reclaim £2,730 from Halifax. It initially refused to refund the couple, both 38, but last month offered to pay them £1,365 – half their claim.

Nicola said: “We were surprised when Halifax made the offer and were tempted to accept. But we didn’t realise this would prevent us from making a further claim for full compensation. We are now unsure what to do next.”

Claims specialists have accused the FSA of rewarding the underhand tactics of the high-street banks, which have been allowed to continue to levy the disputed penalty fees of up to £39.

Michael Goldstone at Conkers said: “Allowing banks to put further claims on hold has left these savers between a rock and a hard place. It is very unfair and I suspect many will accept a sub-standard offer rather than risk getting nothing or waiting for years, saving the banks tens of thousands of pounds.”

The FSA has said that it will review the claims freeze at the end of next month. But campaigners argue it should scrap the waiver now or impose tighter restrictions on the banks.

Martin Lewis of Moneysavingexpert, a consumer website, said: “At the moment everything is working in the banks’ favour. The suspension of claims means they are not having to pay out any further refunds, yet they are still able to rake in huge amounts of money.

“The FSA should either revoke the waiver, so people can pursue their claims again, or banks should also be suspended from levying penalty charges until the court case has been resolved.”

On Friday a judge at Luton county court ordered Barclays to stop levying charges on a customer until the test case is settled. Judgments made in county courts do not set legal precedents, so banks, including Barclays can continue charging these fees to other customers.

In the meantime, Lewis believes savers should reject refunds that are substantially less than they claimed. He said: “My advice, if you have received a percentage offer and the money is paid directly into your account, is to write back to your bank and say you do not accept the money as a full and final settlement.”

If you are thinking of making a new complaint, your claim will not be processed but it may be still worth doing. You can only claim for charges going back six years, so if you incurred big penalties more than four or five years ago you could be deemed “out of time” if you don’t act soon.

Moneysavingexpert, the Consumer Action Group and Penalty Charges have launched a petition calling for Gordon Brown to support a bank charges reclaiming charter. To sign up visit petitions.pm.gov.uk/bankcharter.