Transport Secretary Chris Grayling has accused trade unions of driving the 3.1% increase in rail fares.
Mr Grayling told the BBC unions had demanded “higher pay rises than anyone else” and threatened strikes if they did not get them.
The Rail, Maritime and Transport Union said it was “scandalous” that Mr Grayling was trying to blame workers.
Rail fares have increased by an average of almost 3% in Scotland and 3.1% in England and Wales.
Labour leader Jeremy Corbyn called the increase a “disgrace” and said it “drives people away from public transport”.
Mr Grayling told the BBC Radio 4’s Today programme: “The reality is the fare increases are higher than they should be because the unions demand – with threats of national rail strikes if they don’t get them – higher pay rises than anybody else.”
In August, the government asked the train operators and unions to use a different, lower, inflation measure to set pay and fare increases – which the RMT opposed.
Mick Cash, general secretary of RMT, accused Mr Grayling of trying to blame rail workers for problems “caused by privatisation of the railways”.
Mr Grayling also said that the government had made a “record investment” in rail.
He announced that a new railcard extending child fares to 16 and 17-year-olds in full-time education or training will be available by September.
A discount railcard for 26 to 30-year-olds went on sale at 12:00 GMT. Like the existing card for 16 to 25-year-olds, it costs £30 and reduces fares by a third.
Initial demand for the new railcard was high – National Rail’s online queuing system showed wait times of more than an hour.
The rise in England and Wales – the highest since January 2013 – will see the price of some annual season tickets go up by more than £100.
Some fares in London will stay the same after a decision by Mayor Sadiq Khan to freeze Transport for London prices. However, on average Travelcards and price caps have increased by 3.1% in London.
The rail industry says 98p of every pound spent on a ticket is invested back into the network.
But Wednesday’s price hike was called “yet another kick in the wallet” by campaign group Railfuture.
Shadow transport secretary Andy McDonald said the latest increases were “an affront to everyone who has had to endure years of chaos on Britain’s railways”.
He also called on the government to freeze fares on the “worst performing” routes.
Campaigners held protests against rises outside stations across the country.
Analysis from the Labour Party of more than 180 UK routes claimed that since the Conservatives came into power in 2010, the average commuter is paying £786 more for their annual season ticket.
The increases come despite one in seven trains being delayed by at least five minutes in the past 12 months – the network’s worst performance since September 2005, according to the Press Association.
Chaos caused by new timetables from Northern and Govia Thameslink added to problems of extreme weather, strikes and signal failures hitting routes across the country.
Around 45% of fares are regulated by government, and capped at July’s retail price index inflation figure – 3.2%.
Other increases are decided by the train companies.
‘Value for money?’
ScotRail defended its average increase of 2.8%, despite breaching performance targets with cancellations throughout November and December.
The company said its fare rises were lower than in England and Wales, adding that it was investing “millions of pounds to build the best railway Scotland has ever had”.
Robert Nisbet, regional director of industry body the Rail Delivery Group, said investment was at its highest level since the Victorian era and “that money has to come from somewhere”.
He said by 2021 there would be 7,000 new carriages across the country and 6,400 new services.
The UK’s railways are predominantly funded by customers’ fares: last year’s figures from the Office of Rail and Road show they yield £9.7bn, while the government provides £6.4bn – excluding loans from Network Rail.
However, almost a third of the government funding was given specifically to the HS2 high-speed rail project.
Campaign group Transport Focus said only 45% of passengers were satisfied with the value for money of their tickets.
Chief executive Anthony Smith told the BBC: “The industry should be becoming more efficient and that efficiency should be passed back to passengers to reflect a poor year.”
The Department for Transport has commissioned former British Airways chief executive Keith Williams to carry out a review of Britain’s railway network – including fares.