Co-operative Bank customers have hit out at the lender after a glitch led to payments being taken twice from some business accounts.

Customers said they had been pushed into their overdrafts because of the problem, which has resulted in previous payments, sometimes made several weeks before, being duplicated.

One business owner said on social media that they had been left “almost £5,000 down”, while another claimed they had only realised that money had been taken when they could not buy petrol. Others have complained that the incident has meant they have been unable to buy supplies and run their businesses.

The bank said: “We are aware there are a small number of SME account holders who have duplicated payments showing in their balances and are in the process of correcting this issue.

“We apologise for any inconvenience caused and are supporting customers during this period.”

The Guardian understands that if any customers have suffered financial detriment as a result of the problem, the Co-op Bank is looking to remediate accordingly.

The Co-op Bank has almost 5 million customers, including 95,000 accounts for small and medium-sized businesses. The Guardian has contacted the Co-op to ask how many customers have been affected.

After the incident, other customers complained on social media that they had been stuck on hold on the bank’s support line for long periods.

One customer posted on X: “You’ve destroyed my working day due to this, I’ve ended up stranded at a van hire office for two hours, having been stuck on hold on the phone to you for over an hour, with no pick up.”

Another business tweeted on Tuesday night: “A full 24 hours in and account still in debit, not a single update, business not able to pay suppliers, I’m using my personal account to get by, this is very poor service indeed.”

Despite apologising on its X account, the company’s website did not have any details about the problem.

Coventry Building Society said in April it would buy the bank from its hedge fund owners in a deal worth £780m. Coventry said this could result in the Co-op Bank brand disappearing within several years.

In March, Co-op announced it would look to cut 400 jobs in a bid to cut costs and restructure the business.