Trains on the Alton to Waterloo line are expected to be disrupted until Friday evening after engineering works overran.
An equipment failure has been blamed by Network Rail for delays to overnight works between Woking and Byfleet and New Haw.
This has affected services between London Waterloo and Southampton, Salisbury, Portsmouth, Basingstoke and Alton.
South Western Railway (SWR) said on X (formerly Twitter) that services are likely to be delayed, cancelled or revised until the end of service on Friday.
Network Rail apologised for the disruption and said the machinery they needed to use for the overnight work failed.
It said a stressing kit got stuck on one of the rails and engineers were unable to release it as normal until all the hydraulic fluid has been drained from it.
The railway line reopened at 8.15am on Wednesday but SWR said trains will continue to be disrupted as trains and crew members are in the wrong places.
Network Rail’s Louise Greaves told BBC Radio Surrey: "It has been an incredibly difficult morning for passengers.
"We use this equipment every night and it is usually fine, but unfortunately this time it failed.
"If we had opened the railway lines, the pressure would have been too high and could have caused the equipment to come off the tracks, which would have been a danger for trains and staff on site.
"Safety is our number one priority."
Passengers who reach their destination 15 minutes late or more are eligible to make a claim under the Delay Repay scheme.