As the rush hour began on Monday morning, it was clear that Britain’s biggest rail timetable change ever in peacetime had been botched.

The new schedules on Great Northern, Thameslink, Southern took effect at 2am on Sunday. Passengers using hundreds of stations in London, Surrey, Sussex, Kent, Hertfordshire and Cambridgeshire have had their train times comprehensively changed. One in four UK rail users are affected.

The key change is that trains from across the southeast will be funnelled through a central core between London Blackfriars and St Pancras International, the Eurostar hub

During Sunday dozens of trains were cancelled because of what the franchise holder, Govia Thameslink Railway (GTR) called “an operational incident”.

While the rain firm refused to disclose more, it appeared that insufficient drivers had reported for duty; Sunday working is still voluntary on many train operators.

But as Monday morning dawned it was clear that the plans had not survived first contact with the rush hour, and that tens of thousands of commuters were going to endure a frustrating start to the working week.

Between 7am and 8am, 11 trains on the line north and south from St Pancras were cancelled, with a points failure adding to the problems. Three trains in a row on the key link from East Croydon to London Bridge were axed, with passengers told only: “This train has been cancelled because of an operational incident.”

The main issues appear to be on the central core. Before the changes took effect, the RMT union had warned of “disastrous consequences” because of the pressure on the section between London Blackfriars and St Pancras.

Paul Plummer, chief executive of the Rail Delivery Group, which represents the rail industry, said: “Retiming over 100,000 services across a weekend is a huge operational challenge, and as a result there may be some teething problems.

“We therefore advise customers to check their train times before they travel on the National Rail Enquiries website, or download the National Rail ‘alert me’ app for updates.”

The National Rail Enquiries website revealed that the planning process was completed only three-and-a-half weeks ahead rather than 12, “due to the vast undertaking of rewriting the timetable from start to accommodate the large network”.

“Part of this process is defining the scope of engineering work to the track, which affects the deployment of trains and train crew and the access they have to train maintenance depots.

“This means they have had less time than normal to re-plan the driver allocations as well as the train stabling and maintenance requirements.

“The train operators thank you for your patience and apologise for the inconvenience caused during the upcoming weeks.”

As well as the short-term issues, commuters in some towns are complaining of longer-term problems.

Travellers from Harpenden, Hitchin and Royston in Hertfordshire say the number of rush-hour trains serving their stations has been sharply reduced, and that timings are significantly worse than before.