Network Rail is investigating claims that engineering contractor Jarvis entered falsified documents over track work.
The allegations relate to work being carried out on the West Coast Main Line between Stoke and Macclesfield.
Jarvis admitted it had laid some of the track incorrectly, leading to speed restrictions being introduced this week. But the engineering firm strenuously denied allegations of impropriety.
“We would refute any allegations that documentation had been falsified,” a spokeswoman said.
“Any Jarvis employee found to have deliberately falsified documentation could expect to be dismissed and possibly prosecuted,” she added.
The spokeswoman admitted that “incorrect stressing methods had been used” on the sections of track between Macclesfield and Stoke.
But she added that official certification relating to quality and other checks were yet to be entered.
The problems with the stressing carried out by Jarvis puts the track at risk of cracking in cold night-time conditions. Network Rail confirmed an investigation was taking place after a journalist bought the allegations to its attention.
“These are serious allegations and Network Rail is treating them accordingly,” a spokesman said.