Terence Wray was repairing a fault on the track at Cheshunt Junction in Hertfordshire in March 2010.
In order to let an approaching train pass, Wray moved to what he believed was a position of safety on the track.
But the train diverted to the line on which he was sheltered and struck him, causing serious injuries.
St Albans Crown Court heard that an extensive Office of Rail Regulation investigation found the work at Cheshunt Junction had not been properly managed.
The court heard evidence that the work was inadequately planned by unqualified personnel and, despite safer methods being available, was scheduled to be carried out while trains continued to run.
Tom Wake, ORR’s Deputy Director Railway Safety, said: “The safety of track workers, and all those working on Britain’s railways, is a top priority for ORR.
“Where maintenance work takes place it should be planned, well managed and not place workers in unnecessary danger.
“In this case, Network Rail’s management and planning for maintenance of the track at Cheshunt Junction, Hertfordshire was not good enough. The company’s failures caused the entirely avoidable and life-changing injuries for its employee Terence Wray.
“Since the incident Network Rail has reduced the number of works taking place on tracks whilst trains continued to run, further protecting the safety of its employees.
“The regulator will continue to monitor the company’s management of rail maintenance and we will always step in when required to protect those working on, and using, the railway.”