Passengers were told they could get their money back on annual passes when the lockdown at the end of March forced them to stop travelling to work.
The normal 28 working days’ deadline for refunds was doubled to 56 days because of the huge number of applications.
But with many now being encouraged to return following the partial lifting of the “stay at home” order, they face having to buy new passes without having had their money back.
Watchdog London TravelWatch said complaints about season ticket refunds had surged fivefold in recent weeks. Chairman Arthur Leathley said: “We want the industry to turn these refunds around much more quickly. Some operators have been able to, so if they can, why can’t all of them? This is money that people need to put food on the table.”
One long distance commuter, design director Lee Bearton, who pays £6,600 a year for his season ticket from Milton Keynes, said: “I had to fill in a long form and send them a picture of my season ticket cut in half.
“London Northwestern initially said I would be refunded within 28 days, but on the 27th day I said ‘when is it coming?’ And then they said it would take up to 56 days.
“I face the situation where I might be going back to the office and have to fork out another £6,600. It’s a hell of a lot of money to hold on to for more than two months.”
A spokesman for London Northwestern said: “The unprecedented government restrictions on travel resulted in a huge increase in requests for season ticket refunds, which has impacted our processing times.
“We have brought in new processes and redeployed staff to deal with the demand. We have already processed thousands of refunds and reassure our customers we are working hard to issue the remaining refunds as soon as possible.”
The Rail Delivery Group, the industry body that represents train operators, said it had been deluged with requests for season ticket refunds and had so far processed 109,000, more than the 79,000 in the whole of 2019.