Passengers on some of the busiest rail routes in England have been warned not to travel because of overrunning engineering works.

No South Western Railway (SWR) trains were operating on Monday morning between Surbiton and London Waterloo – the UK’s busiest railway station.

It is the latest disruption to hit the rail company after a spate of problems involving signal and points failures. A long-running dispute over the role of guards on trains has also crippled services because of strikes.

Passengers were told: “We have been informed of overrunning Network Rail engineering works between London Waterloo and Surbiton. This means that trains cannot run between London Waterloo and Surbiton.

“Customers are advised not to travel. Woking, Surbiton, Raynes Park and Earlsfield stations are currently closed. Disruption is expected until the end of the day.”

SWR added that Network Rail’s engineering works were not expected to be cleared until 8.30am “at the earliest” – four hours later than planned. It said: “Until the works clear no trains can leave Wimbledon or Clapham Junction depots.”

Normally packed commuter trains were cancelled, leaving tens of thousands of passengers stranded.

Southern services between East Croydon and London Victoria were also disrupted because of overrunning engineering works.

The Rail, Maritime and Transport (RMT) union called for the resignation of the transport secretary, Chris Grayling, because of the latest travel chaos.

Its general secretary, Mick Cash, said: “The chaos into Waterloo this morning is just another example of the fragmentation and division on Britain’s privatised railways where maintenance schedules and budgets are hacked to the bare bones while private operators like SWR are left with a free hand to rob the network blind in the name of profit.

“What we need is reintegration and a coherent system with all elements of the rail operation working together in one publicly owned framework, with investment rather than exploitation as the watchword.

“While the crisis on our railways deepens, the transport secretary, Chris Grayling, is markedly absent while he ponders his self-interest and a possible resignation from the May government. He should go, and he should go now.”

He added: “With Waterloo closed and London and the south plunged into rail chaos this morning, RMT is now picking up reports of wholesale cancellations on Northern Rail due to a shortage of fleet, reinforcing the point that this is a national crisis.

“Both Arriva Rail North and South Western Railway have a track record of hacking back on staffing and budgets to bump up profits and today’s Monday meltdown is the consequence of their actions. The case for public ownership is now overwhelming.”

Anthony Smith, chief executive of the independent watchdog Transport Focus, said: “Passengers rely on the railway - this morning tens of thousands of passengers coming into Waterloo could not. While engineering and improvement works need to be done, such late notice of the fundamental problems on the approaches to Waterloo this morning is unacceptable.

“A quick, thorough review of the problems uncovered in the engineering works and the passenger information put out should be carried out and published so that lessons can be learned. In the meantime, passengers should claim for compensation and make sure their voice is heard.”

A Network Rail spokesman said: “We would like to apologise for the disruption to passengers’ journeys on South Western this morning. This is due to overrunning engineering works in the Hampton Court area. Currently all four lines are blocked and no trains are able to run between Surbiton and Waterloo. Network Rail workers are on site and hope to resolve the issue as soon as possible.

“Passengers are urged to check before they travel via National Rail Enquiries or with their train operator.”

An SWR spokesman said: “Passengers are asked to delay the start of their journeys this morning as all lines from Surbiton into Waterloo are blocked due to overrunning engineering works.

“Network Rail engineers are working hard to reopen the lines as soon as possible but passengers are advised to check the website before starting their journey as currently services are having to be cancelled and diverted.”