Average rail ticket prices have risen by 3.4% across the UK, in the biggest increase to fares since 2013.
Protests are under way at some 40 stations, as many commuters see their season tickets go up by more than £100.
Campaigners warned that many people were being “priced off” UK railways, while Labour described the network as “fractured, expensive and complex”.
The Department for Transport said price rises were capped in line with inflation and improved the network.
Commuter routes that are now more expensive include Liverpool to Manchester (up £108 to £3,152), Maidenhead to London (up £104 to £3,092) and Elgin to Inverness (up £100 to £2,904).
Fare increases to regulated fares – which comprise about half of all tickets – are calculated using the previous July’s Retail Prices Index (RPI) measure of inflation.
Since 2007, the financial burden of running the rail system has increasingly fallen on passengers, after the government decided taxpayers as a whole should pay less via subsidies.
Fares used to account for about half the cost of running our trains, whereas now it is about 70%.
Paul Plummer, chief executive of industry trade body the Rail Delivery Group, said the fare changes would provide cash for better services and investment, including the Thameslink and Great Northern rail upgrades.
“None of us obviously want to pay higher fares,” he told BBC Radio 4’s Today programme, adding: “Fares are actually underpinning massively required investment.”
But Bruce Williamson, of campaign group Railfuture, has called for the lower Consumer Price Index (CPI) inflation measure to be used for regulated fare increases.
Mr Williamson argued that if CPI had been used rather than RPI since 2004, rail fares would be 17% lower.
He said people were being priced out of getting to work, with British rail fares among “the most expensive in Europe”.
Commuter Sarah Beer, from Lingfield in Surrey, said her rail commute to London of nearly £4,000 a year was an “extortionate amount of money”.
“It is like watching the Great Train Robbery all over again,” she told Today.
“What I cannot grasp, in this day and age, is that all we ask for is a reliable train service.”
On the first working day of 2018, many commuters took to social media with their reactions to the increases.
Stephen Joseph, chief executive of the Campaign for Better Transport (CBT), accused the government of choosing to “snub rail passengers” while fuel duty continued to be frozen.
“The extra money that season ticket holders will have to fork out this year is almost as much as drivers will save,” Mr Joseph said.
London Mayor Sadiq Khan, who has frozen fares across the capital’s TfL nework until 2020, questioned why ticket prices were going up elsewhere.
“It’s a scandal that the government are allowing failing private train companies to increase rail fares again,” he said.
Meanwhile Mick Cash, general secretary of the Rail, Maritime and Transport Workers (RMT) union, warned people were being “priced off” UK railways.
“People’s wages aren’t going up the same as fare rises,” he told BBC News, adding that public ownership of the railways was a “necessary” step.
The union has planned fare protests in stations across the country, including at King’s Cross in London, Leeds, Manchester Piccadilly and Cardiff, with separate protests planned for 3 January in Scotland.
Andy McDonald, the shadow transport secretary, said: “We have a fractured, expensive and complex system – we’re wasting money”.
A spokesman for the Department for Transport said it was investing in the “biggest modernisation of our railways since the Victorian times”.
He said: “This includes the first trains running though London on the Crossrail project, an entirely new Thameslink rail service, and continuing work on the transformative Great North Rail Project.”
Mark Carne, chief executive of Network Rail, said passengers would see a “huge change” in the coming year due to investment in rail networks.
“We all share the desire to try to keep fares as low as possible,” he told BBC Breakfast. “My job is to run the network as efficiently as possible.”
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