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Southeastern says disruption on its services from Kent into London will last for the rest of the week.
Investigators are still trying to work out how a freight train came off the tracks near Lewisham yesterday morning.
The main line into the capital is partially closed while repairs are carried out.
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Two wagons of a 1km-long freight train derailed at Lewisham in the early hours yesterday.
Southeastern says the disruption is likely to continue into tomorrow as the recovery continues.
Network Rail says teams have been working round-the-clock since the derailment, and are using cranes and jacks to get the two derailed wagons back on the tracks and moved from site.
The extent of the damage caused by the wagons means that a 50m stretch of railway needs to be completely rebuilt. It is estimated that the work will take several days to complete.
Andy Derbyshire, chief operating officer for Network Rail’s south east route, said: "We know that this incident is disrupting many peoples’ journeys and I’m sorry it will be a few days yet before services return to normal.
"We are doing everything we can to get the site clear and our repairs under way as quickly and safely as possible.
"We need to completely rebuild more than 50m of railway from the foundations up, just a few metres from one of the busiest railway lines in the south east.
"This is a significant job but we’ll be working round-the-clock until the work is done and trains are back up and running for passengers."
Richard Dean, train services director at Southeastern, added: "This derailment has had a huge impact on the services we have been able to run over the last few days and unfortunately, due to the level of work needed, this will continue for the next few subsequently the days to come.
"It has been very difficult for our passengers and we urge those delayed for 30 minutes or more to claim Delay Repay compensation, which will be doubled until the issue is resolved.
"We would like to thank you to those who travel with us for their continued patience while the emergency repair work is completed as quickly as possible during this time.
"We would also ask our passengers to please continue to checking before you travelling and to allow more time for your journeys.
"Information will be available at stations and online, including on Twitter where our team will be sharing the most up-to-date information."
Here's how the delays affect you
Trains on the following routes will be revised:
The following evening peak services from Cannon Street to the Medway Towns will be revised:
There is no service on the following route:
The following stations will have a reduced service:
Trains on the following routes will run as normal:
Yesterday, passengers took to social media to express their frustration after trains were running late, with commuters tweeting pictures of queues at Dartford.
Network Rail engineers have been on site working to re-rail the two wagons so the train can be moved and assessment of any damage and repairs can be made.
The rail firm said services through the affected area will be unable to resume this week, but updates will be issued when they become available.
Tickets are being accepted on London Buses, Overground, Underground, DLR, Trams and Thameslink services.
Network Rail said no one was hurt when the train slipped off the tracks.
Listen to kmfm for live travel updates.