Rail passengers in the north of England are facing large increases in the cost of travel after the introduction of peak evening fares on train services from Monday.

The new rules mean passengers in Greater Manchester and parts of urban Yorkshire will no longer be able to buy off-peak return tickets for travel between 4pm and 6.30pm. Peak or "Anytime" tickets cost typically 40-50% more than off-peak fares.

The chancellor, George Osborne, partly softened the blow by announcing on Sunday that regulated fares rising in January would not go up in real terms. He withdrew the right of train companies to raise fares on individual routes – known as "the flex" – following Labour's 2015 election pledge to abolish it. It means all fare rises will be capped at 2.5% in 2015.

Some passengers are already seeing the cost of their journeys rise by much more. An £11 peak return from Rochdale to Wigan will apply to travellers on evening peak journeys from Monday, rising from the previous off-peak fare of £4.20 — a 162% increase. Commuters from Osborne's Tatton constituency will need to pay between 34% and 52% more to travel in the new peak times.

Northern Rail, which operates the majority of services in the region, about 2,500 trains each day, has been pressed by the Department for Transport (DfT) to raise extra revenue as the government aims to cut its subsidy, the largest paid to any train company. Sixty-nine percent of Northern's costs was covered via public subsidy in 2012-13. At the same time it paid dividends of £36m to its shareholders.

Northern has been run since 2004 by a joint venture between outsourcing firm Serco and Abellio, which is part of the Dutch state-owned rail group. Their contract was extended for two years until 2016 following the West Coast fiasco, involving failings in the tendering process by the Transport Department. Serco has withdrawn from the partnership for the next Northern franchise bid, though Abellio is shortlisted. The other two shortlisted bidders are Arriva, a Deutsche Bahn subsidiary, and Govia, part-owned by the French SNCF.

Northern said most passengers will not pay more, as many have season tickets or already purchase a top-price return as they travel in the morning peak.

Company insiders argue that the subsidy figure is inflated by arbitrarily high track charges. Even some independent transport campaigners agree that the stated subsidy does not reflect the true state of investment. Martin Abrams of the Campaign for Better Transport said: "The DfT's extension of peak fares on Northern is part of an incoherent strategy to make existing passengers pay more for outdated services instead of investing in better quality rail for the future across the region."

Northern said the higher fares could ease crowding for commuters, and its fare policy now matched those in London. Critics say services do not operate at the frequencies experienced in London, and work-life patterns in the north mean most passengers need to travel at peak times.

The shadow transport secretary, Mary Creagh, said the fare rises were "a direct result of the government's West Coast franchise fiasco, and commuters travelling to Leeds, Manchester, Bradford, Sheffield and Newcastle are paying the price. People shouldn't have to choose between paying more or waiting until after dark to travel."

Many services are operated on ageing Pacer trains and passengers fear the government is dodging a pledge to update them. A DfT spokesman said: "The Pacer trains have served the railway well, but we recognise that they fall short of many passengers' expectations. That is why we are requiring all bidders to submit proposals for the replacement of these trains."

Rail expert Paul Salveson, a visiting professor at the University of Huddersfield, said the wording of the franchise prospectus is "suitably vague" and does not compel the new franchisee to replace them. Instead, Salveson thinks Northern Rail users are more likely to be given refurbished District Line tube trains from London.

Commuters expressed anger at the rise. Michael Taylor, a regular commuter from Stockport to Manchester Piccadilly said: "I despair at Northern Rail, but I also feel a rising anger, more so as I spend time in London. While London is getting Crossrail, has upgraded the Overground, we get more of these cattle trucks."

The RMT is holding protests at mainline stations to highlight the fare increases and feared cost-cutting measures, including job losses and removing guards from trains. The union's acting general secretary, Mick Cash, said it was "a savage kick in the teeth for people already struggling with the burden of low pay and austerity".