A multimillion-pound tax on poorly performing rail companies should be used to freeze fares for passengers hit by weeks of disruption, Labour says.

Andy McDonald, the shadow transport secretary, backed the move as another major fares rise is set to be confirmed this week, despite disruptions on several lines that have affected thousands of passengers.

An increase of more than 3% is expected to be applied to some fares in the new year, including season tickets. Fare prices are linked to the rate of inflation recorded for July, which will be unveiled on Wednesday.

McDonald said three train companies affected by major disruption this year – Govia Thameslink, Arriva Rail North and First Transpennine Express – should fund a fare freeze as a “gesture of goodwill” to passengers. Labour said it backed the idea of profits tax as a one-off move.

The chief executive of the company that owns Govia Thameslink quit this year after weeks of cancellations and delays on its services in south- east England. More than a month of disruption followed the introduction of new timetables in May. Chris Grayling, the transport secretary, has faced calls to strip the company of the deal to run the trains.

Delays and cancellations also affected services in northern England run by Arriva Rail North. It has blamed driver shortages, as well as the new timetables. First Transpennine Express blamed signalling failures, trespassers and congestion following the timetable change. An inquiry has been launched into how the chaos unfolded, with the results due to be published before the end of the year.

Under Labour’s plan, a freeze would be applied to the regulated fares charged by the three companies, which include season tickets and peak-time tickets. The party said the move would cost Arriva Rail North £4m, Govia Thameslink £19.5m and First Transpennine Express £3m.

“Carry on Grayling isn’t funny any more. The public has lost faith and trust in the way our railways are being run on his watch, yet the transport secretary remains in denial. Labour is calling on the government to freeze rail fares on the routes most severely affected by the timetable changes,” McDonald said. “This freeze should be funded by a windfall tax on the profits of the train operators involved.”

However, industry insiders said the imposition of an emergency tax could have serious unintended consequences. One said that, because fares rise every year with inflation, passengers could face an even steeper increase in 2020 as a result of a temporary freeze next year.

Paul Plummer, chief executive of the Rail Delivery Group, which represents the public and private rail organisations that form the rail industry, said: “We are sorry for the recent disruption experienced by some of our customers. Northern, Transpennine Express and GTR are offering additional compensation to people who were impacted, including those on season tickets, and we strongly encourage customers to claim.

“Operators only get the chance to run a franchise if they offer the best value to taxpayers and any profits depend on successful delivery for customers. With 98p in every pound spent going back into the railway, fares are supporting a once-in-a-generation investment programme that will change and improve services for the benefit of our customers, local communities and the economy.”

A spokesman for the Department for Transport said: “This is the sixth year in a row where this government will cap regulated fares – like most season tickets – in line with inflation.

“Any fare increase is unwelcome, especially for those who have experienced unacceptable levels of disruption caused by the new timetable in May, but we are compensating customers on affected routes with up to the cost of one month’s travel.

“Fare increases are helping to pay for the biggest upgrade of the Great Western main line since Brunel built it 150 years ago. We are transforming travel in the north with a £3bn upgrade of the Transpennine route and providing an extra 500 carriages with space for 40,000 extra passengers and 2,000 extra services each week. We will also be opening London’s Crossrail and are in the process of delivering an entirely new Intercity express programme.”