Delays were initially blamed on major signalling problems
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Commuters have suffered major delays after two trains came within 150 metres of a collision.
One packed passenger train was held outside High Brooms station in Kent for three-and-a-half hours following the incident.
Network Rail confirmed two trains, neither of them carrying passengers, had ended up on the same section of track near Tunbridge Wells.
Tests are now being carried out on track and signalling equipment - but Network Rail said there had been no chance of a crash.
Passengers in Kent and Sussex suffered serious hold-ups on Wednesday after the incident.
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Neither train was in passenger service and there was no risk of collision
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Disruption continued on Thursday, with a replacement bus service operating between Tonbridge and Hastings and a reduced rail service from Tonbridge to London.
Connex had initially blamed the delays to trains between London and Hastings on a signals failure.
But Network Rail issued a statement confirming the stoppages were caused by investigations into how the two trains came to be so close together on the track.
Heavy delays
According to Network Rail, at 2000 BST a train travelling at 20 mph moved onto a section of track near Tunbridge Wells, placing it on the same stretch as an empty stationary train.
"Neither train was in passenger service and there was no risk of collision," the statement said.
"Network Rail immediately began a full investigation, involving testing of track and signalling equipment.
"As a result, passenger services in the area were subject to heavy delays throughout the evening."
Both Network Rail and Connex apologised for the delays experienced by passengers.
The disruption to services was expected to carry on into Thursday while inquiries continued.
The Health and Safety Executive's Rail Inspectorate confirmed they were investigating the incident.
Connex was stripped of the franchise to run trains in the region earlier this year because of poor financial management and will cease to operate services from 31 December.