A train operator has apologised for disruption caused to passengers after the largest timetable change across Britain for decades was introduced.

Every train run by the UK’s busiest franchise, Govia Thameslink Railway (GTR) – which consists of Southern, Thameslink, Great Northern and Gatwick Express – was rescheduled from Sunday.

The firm had warned that services could be disrupted as the new timetable was introduced.

But some passengers were left frustrated and confused by cancelled services.

Great Northern, which runs trains north-east out of London to places including Cambridge and Peterborough, said on its Twitter feed: “A reduced Great Northern service is expected until the end of the day.

“A short-term amended timetable is in place across the Great Northern network. This is resulting in a reduced service operating with trains being cancelled or revised.

“Disruption is expected until the end of the day.”

Passengers complained to the firm on social media saying they had been told services had been cancelled due to an “operational incident”.

A GTR spokesman said: “We are introducing the biggest change to rail timetables in a generation and, as we have been informing passengers, we expect some disruption to services in the initial stages.

“This is a significant logistical challenge as we make rolling incremental changes across more than 3,000 daily services.

“We apologise to customers for any inconvenience caused during the initial stages of the timetable change.

“The improvements we are making will lead to a significant boost in capacity with a 13 per cent increase in services across the GTR network immediately.”

Passengers have been warned that disruption caused by the implementation of the timetable could continue into Monday.

More than four million trains across Britain were rescheduled from Sunday in the largest timetable change in living memory.

The number of alterations is seven times larger than normal due to the introduction of new trains and services following billions of pounds of investment.

The shake-up is designed to increase overall frequencies and reliability, but some passengers will find their regular journeys are no longer possible.

The new GTR timetable was developed from scratch and was designed to tackle existing issues by extending stop times at busier stations and increasing turnaround times at destination stations.

Many of the timetable changes are a result of the £7 billion invested in the Thameslink programme in the South East, including rebuilding London Bridge station, new trains and track improvements.

There will be almost 400 additional GTR trains every day.

Some passengers in a number of locations complained they will be served with fewer or slower services, including in Hertfordshire, Bedfordshire, Kent, East Sussex and Surrey, where many people pay several thousands of pounds for annual season tickets to London.

The Rail, Maritime and Transport union said it had received widespread reports from the front line of severe disruption to services on the first day of the new GTR timetable.

The union voiced “real fears” that ‎routes will be on a knife edge on Monday morning when passengers return to work.

RMT General Secretary Mick Cash said: “As RMT warned the new timetable on GTR is placing massive additional strains on infrastructure and staffing levels that are already struggling to cope with current capacity.

“The company are winging it with potentially disastrous consequences. RMT has warned repeatedly about the pressure on the central core through the middle of London which is crucial to the delivery of these plans and those fears are being borne out from reports coming in today.