Thousands of rail passengers could be left out of pocket in this year’s great Christmas getaway, the transport watchdog has warned, after railcard applications and renewals were delayed when the national website crashed.

Over the last two weeks, Transport Focus has been inundated with complaints from worried passengers who need to travel over the holiday period but have been unable to buy or renew railcards that give them discounts – typically of one-third – on train tickets.

On the eve of the mass festive exodus starting this weekend, the watchdog is urging the industry to take urgent steps to fix the problem. In the meantime it is seeking reassurances that staff will be advised to treat passengers affected “with understanding” and to not issue penalty fare notices or charge full fares if passengers have bought but not received their railcards.

At the end of November, the Rail Delivery Group (RDG) representing train operators – which manages the railcard scheme – switched the national customer contact call and email systems to a new supplier, but the website crashed and the RDG has since been unable to reliably fulfil orders.

As a result, calls to the RDG contact centre increased significantly (from about 500 to 3,000-plus calls per day), increasing the time before the phone was answered. As passengers have struggled to get through on the phone, calls to Transport Focus have increased. About 5.3m railcards of various kinds are in issue in the UK, and digital as well as traditional paper railcards are affected.

In a letter to Paul Plummer, the chief executive of the RDG, sent by Anthony Smith, the chief executive of Transport Focus, and seen by the Guardian, Smith says he is writing to express his concern “about the passenger implications of changes to the industry’s railcard support arrangements”.

He said: “Passengers have been left inconvenienced, worried about where they stand with staff checking tickets and potentially left out of pocket as a result of these problems.”

“The rail industry needs to demonstrate that it is doing everything possible to fix this, provide the correct advice online and to station staff and promptly reimburse anyone impacted. Anyone that has bought a railcard but has yet to receive it should be in no doubt that they can still travel and that they will be treated with understanding.”

Smith is seeking reassurance from the RDG that all train company websites will provide advice to passengers about what they should do if they have been unable to buy or have not yet received a railcard. He also wants to know that train companies have issued guidance to “frontline” staff and those in customer relations teams about how passengers should be treated.

Smith said no single issue had caused more passengers to contact Transport Focus since the setting-up of the rail passenger ombudsman a year ago – despite other major disruption including the chaos caused by twice-yearly timetable changes.

Angry comments cited by Transport Focus included one person saying that they had been stuck on the phone for two hours and another saying it was “simply impossible” to reach Railcard, with emails and calls going unanswered.

Jacqueline Starr, the chief operating officer of the RDG, said: “We recently undertook essential, planned maintenance to the railcard website to improve existing technology and enable a much quicker, smoother buying process. While 99% of customers are not experiencing problems, we are aware there are still some outstanding technical issues and we offer our sincere apologies to anyone who has had difficulties purchasing railcards recently.”

Advising people experiencing problems to buy their card at a station if possible, Starr added: “We have responded to Transport Focus to confirm that as a priority we have taken a number of steps to help people experiencing problems and we are committed to ensuring that nobody will be left out of pocket.

“Steps we have taken to help customers include bolstering our team to double its normal size with staff working round the clock. We have briefed frontline staff to accept email confirmations of railcards, asked train operators to provide advice on their websites and installed a customer call-back facility so that people do not have to wait on the telephone.”