UK rail fares will rise by 3.1% in January, the Rail Delivery Group has said.

New fares published on Friday will add hundreds of pounds to many commuters’ annual travel from 2 January 2019.

Fares rose at the start of this year by 3.4%, slightly below the 3.6% cap set for regulated fares.

Passenger groups had demanded a freeze after widespread disruption this year, particularly on Govia Thameslink Railway (GTR) and Northern services, after the botched introduction of a new timetable in May.

Northern fares will rise by slightly more than the industry average, 3.2%. More disruption is expected on Northern trains on Saturday due to an RMT strike, although the company and union are now in talks to avert further planned industrial action.

GTR said its fares would rise at just below 3%, while C2C (2.6%) and Chiltern (2.8%) were implementing the lowest rises among those companies which had revealed their plans.

Britain’s rail fares have grown faster than wages, with real pay having fallen in the last decade.

Regulated fares, which cover about 45% of fares on national rail and include season tickets, off-peak returns and anytime fares around major cities, are set to rise by the level of RPI inflation in July, which was 3.2% this year. The rest – including advance and peak long-distance tickets – can be increased at train companies’ discretion.

Campaigners have criticised the use of RPI – an index that is not widely used in government and is normally higher than CPI. The transport secretary, Chris Grayling, sparked anger in the summer by suggesting rail workers should have pay rises tied to the lower rate if they wished to keep fares lower.

Darren Shirley, the chief executive of the Campaign for Better Transport, said: “Rail passengers have endured enough this year, with botched timetable changes and delays to their journeys which led to the worst punctuality figures for 12 years.

“The government should introduce a fares freeze from January. Any future fare increases should be based on the consumer price index rather than an outdated and discredited measure of inflation. Rail travel should be affordable so passengers aren’t left struggling with the cost of their commute.”

Anthony Smith, the chief executive of the Transport Focus watchdog, echoed calls for a fairer, clearer fares formula based on CPI. “Many passengers, still reeling from summer timetable chaos and frustrated by ‘autumn’ disruption, won’t believe fares are going up again.

“Passengers now pour over £10bn a year into the rail industry alongside significant government investment, so the rail industry cannot be short of funding. When will this translate into a more reliable railway and better value for money for passengers?”

Labour said fares should have been frozen on GTR and Northern, which were particularly affected by the timetabling chaos. The shadow transport secretary, Andy McDonald, said: “With fuel duty frozen over the last eight years while bus and rail fares have been allowed to soar, it’s difficult not to conclude that this government is anti-public transport.”

The London mayor, Sadiq Khan, confirmed tube and bus fares would not rise for another year – although price caps and travelcards, which can include rail travel in the capital, will go up by 3.1%.

Paul Plummer, the chief executive of the Rail Delivery Group, said: “Nobody wants to pay more to travel, especially those who experienced significant disruption earlier this year. Money from fares is underpinning the improvements to the railway that passengers want and which ultimately help boost the wider economy.”

However, rail passengers who got in touch with the Guardian expressed dismay at the continuing fare rises.

Liam Bradshaw’s fare will rise more than the average, by 3.2% to £346.80 a month in January, to commute from St Albans to London St Pancras. He recently took a job with a small pay rise in the capital. “Due to Thameslink’s exorbitant fares I’m actually worse off. I’m unable to get a loan from work to cover an annual season ticket. The train is delayed four days of the week and, on the weekend, services are often cancelled and removed entirely with no forewarning.”

Julie Apps, 49, a bookseller who commutes from Dorking to Guildford, said: “My train has been late every time I’ve taken it – and it is often cancelled, often at the last minute and then we can see it run empty through the station.”

She said that even though she was a part-time worker she was planning to buy an annual season ticket, the price of which is going up to £1,620 and will cost her more money than daily fares, to avoid the stress of buying a ticket from an unmanned station. “Even though they have put in new ticket machines they break down all the time.”

Peter Croasdale, 54, an NHS worker at Guy’s hospital in London, commutes from Preston Park in Brighton to London Bridge on a £3,968 annual season ticket, which is set to rise by £134 to £4,092. He said: “I think my season ticket is good value considering how often I use the service and how far I travel each week. However, as an NHS worker I have had barely any pay rise in the last eight years and the cost of this ticket has increased way beyond any pay rise I may have received.”

Alison Bunce, 44, a video editor, who commutes from Ash Vale, Surrey, to Richmond, south-west London, on South Western, will pay £3,256 in 2019. She said: “Considering the woeful service, the fares are far too high. Every year we are promised that the fare increase will pay for maintenance and so forth, which will mean the service is more reliable. Every year it gets worse.”