Passengers on services travelling both north and southbound were affected, with delays for several hours due to the incident between Retford and Newark Northgate, in Nottinghamshire, on Thursday evening into Friday morning.
At one stage the intruder on the track was said to be on a rail bridge over a river, amid concerns he may fall.
But the incident was finally resolved and brought “to a safe conclusion” with the help of trained negotiators at 3.20am yesterday (Friday April 17).
At one stage nine trains were detained in a holding queue, including Lumo, Hull Trains, Grand Central Rail and LNER services.
LNER said in a statement that it apologised “unreservedly” for the subsequent knock-on delays but explained they were down to trains and passengers being out of place due to the overnight disruption.
David Horne, LNER managing director, said: “I would like to offer my profound apologies to all those whose journeys have been affected.
“We are aware that people were waiting at stations and onboard our trains for a long time, and we know that our customers will have been travelling for important reasons.
“I want to reassure everyone that our teams, both on the ground and behind the scenes, were working hard to get people moving towards their destinations as quickly as possible.
“However, due to the sensitivity of the incident and with the safety of everyone involved being paramount, we could only run our services through the affected area when British Transport Police determined it was safe to do so.
“We thank our customers for their patience and understanding while teams responded to the sensitive situation.”
A British Transport Police spokesperson said: “We were called just before 7:40pm yesterday (April 16) to reports of a trespasser on the line near Retford Railway Station.
“Officers responded alongside Nottinghamshire Police and other emergency services, and a man was located in a precarious position on a bridge.
“A specialist police negotiator also attended the scene to bring the incident to a safe conclusion due to concerns for the man’s welfare.
“At 3.20am on April 17, the man was arrested on suspicion of obstructing the railway and taken into police custody where he remains.”
Gunnar Lindahl, joint operations director for Network Rail and LNER, said: “Our teams worked closely with the emergency services and train operators during this serious and sensitive incident to keep everyone safe and reopen the railway as soon as it was safe to do so.
“We’re sorry to anyone whose journey was affected while the situation was brought to a safe conclusion.
“Once the line was clear, our teams worked quickly to restore services and support operators in getting trains on the move again.”
LNER customers booked on services on April 16 or 17 are eligible to use their existing tickets on any LNER service to their destination up to, and including, Monday April 20.
Customers were advised to make a new seat reservation, for free, via the LNER app, website, or at its Travel Centres.
One of the affected passengers, James Horton, who was on a Kings Cross to Edinburgh LNER service on Thursday evening, finally reached Edinburgh Waverley station several hours later than planned, shortly after 8am on Friday.
But he was full of praise for rail staff on the train on which he was on board.
Taking to social media platform LinkedIn, he said they handled “a difficult situation”, which was not of their making, “very well”.
Mr Horton added: “I can’t thank the staff on the train personally, but credit should be given to them.
“Everyone got to where they needed to be and coffee and water were served all night and morning.”
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