A points failure has caused extra disruption for passengers just hours after the major works at Waterloo started.
Journeys already taking an hour longer from the south are now being slowed down by another 25 minutes according to South West Trains with the issue expected to last until 1500 this afternoon.
An earlier signal problem also halted trains on the Reading line.
Network Rail says its working to make repairs as soon as possible.
Half the station is closed to allow for a massive upgrade with work starting in the early hours of the morning.
The work will last for three weeks.
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Watch our Transport Correspondent Mike Pearse reporting from Waterloo railway station below
By Mike Pearse
Hundreds of thousands of rail passengers in the south are facing the worst ever disruption to services because of more than three weeks of major engineering works at Waterloo that start in the early hours of tomorrow morning.
1,000 engineers will move on site and ten platforms will close. Then the disruption will begin for the 650,000 journeys each day on South West Trains.
The impact will be on services right across the region with Surrey, Hampshire, Berkshire and Wiltshire badly hit.
Around half of South West Trains 1,750 services a day will be cancelled. It means at busy times there could be queues to get into stations of up to an hour. Waterloo and Clapham Junction will be worst hit. There could also be an impact for Southern passengers.
Passengers were asked to take leave or work from home in a massive awareness campaign, the biggest of its type.
But there is anger passengers will get no extra compensation. There have been online petitions and Transport Focus say the rules must be reviewed.
1,000 extra staff will be on hand to help passengers.
The massive work will mean ten platforms will close until after the August Bank Holiday.
The Waterloo International terminal will be back in use to help even with that only half the usual number of services will run.
The work is part of an £800 million project to increase capacity and cut crowding. Platforms will be made longer for new congestion busting carriages and will allow an extra 52,000 seats to be provided on trains.
The lines into Waterloo are the busiest in Europe with passenger numbers doubled over twenty years and continuing to grow.
Estimated waiting times at stations in the London network:
Waterloo - 30 minutes
Vauxhall - 30 minutes
Clapham Junction - 45 minutes
Estimated waiting times across Hampshire:
Estimated waiting times across Surrey: