The annual fares rise is the largest since a 6.1% hike across Britain in 2012, according to a PA news agency analysis of Office of Rail and Road (ORR) data, The Guardian reported.
Rail minister Huw Merriman said the increase is “well below inflation and delayed”, but Labour described it as “savage” and public transport groups claimed passengers are not getting value for money.
Examples of potential increases in ticket prices based on a 5.9% rise include an annual season ticket from Woking to London increasing from £3,664 to £3,880.
An off-peak return from Birmingham to Cardiff will rise from £67.30 to £71.27, while an anytime day single ticket from Liverpool to Leeds will rise from £39.90 to £42.25.
Separate ORR figures show the equivalent of one in 25 train services were cancelled in the year to February 4, representing the worst reliability in records dating back to 2014.
Shadow transport secretary Louise Haigh said: “This savage fare hike will be a sick joke for millions reliant on the Conservative’s broken rail system.
“People already facing soaring taxes and bills will now be clobbered with an eye-watering rise in the cost of the daily commute.”
Latest research by watchdog Transport Focus shows fewer than half of passengers think they get good value for their fares.
Transport Focus’s chief executive, Anthony Smith, said: “After months of unreliable services and strike disruption, it’s clear that too many passengers are not getting a value for money service.
In March last year, rail fares increased across England and Wales by an average of 3.8%.
The cap on increases in regulated rail fares in England, Scotland and Wales is set by the Westminster, Scottish and Welsh Governments respectively.
Britain’s railways have been disrupted by a series of issues such as staff shortages and sickness, industrial action, severe weather and infrastructure failures.
Merriman said: “I understand it has been a difficult year and people are feeling the pinch which is why – through the biggest ever government intervention – we capped the rise well below inflation and delayed it coming into force.”
A spokesperson for Rail Delivery Group, which represents train operators, said: “The government’s decision to hold fares down below current inflation is understandable. It is important that fares are set at a level that is appropriate for both the industry and its customers.