There are delays of up to 40 minutes on trains between Portsmouth and London this morning.
National Rail said the delays to services were caused by the improvement works at London Waterloo, and a points failure at the station on platforms 11 to 15.
A message on the company’s website said trains may be delayed, cancelled or revised.
Services are not expected to return to normal until about 3pm.
SWT said in a message to passengers: ‘As platforms one to 10 were already closed due to planned works, the closure of five additional platforms has caused severe delays.
‘To ease congestion and to return the service to normal, some short-notice alterations will be necessary.’
A Network Rail spokesman said: ‘We know that some passengers experienced difficult journeys home last night. We are sorry that our vital work to expand Waterloo station by 30 per cent over the next three weeks to make room for more and longer trains is so disruptive.
‘Our advice for passengers continues to be to try and travel outside the peak hours, or to work from home or to take some holiday.
‘We know, and have warned, that there will be crowding and queuing systems in operation at busy times and at busy stations and those well-rehearsed plans were brought into use for about an hour last night at Waterloo.
‘While busy, it was controlled with significant numbers of staff on hand to help and advice.’
The improvement works will carry on until August 28, with passengers warned of timetable changes.