GNER could get its way when it comes to the charges firms pay to the Government to run trains on the network.
The York-based firm was angered this week when new "open access operator" Grand Central (GCR) was cleared by the rail regulator to run three daily services from the North-East to London, using the East Coast Mainline, at the same time that its own bid for extra trains was rejected.
It has accused Grand Central of "revenue raiding" and says that, unlike franchised operators, GCR does not have to pay fixed charges or premiums to access the railway.
Now the Department for Transport has indicated it could look at the current system of charging, which GNER says is unfair and needs to be changed.
A spokesman for the Department for Transport said: "We are reflecting on the decision of the regulator and are looking at options for creating a more level playing field."
John Gelson, a spokesman for GNER - which has a ten year contract for the East Coast Mainline franchise for which it will pay £1.3bn - confirmed it wanted the current regime to be reviewed.
Grand Central has dismissed GNER's claims, while confirming it intends to run at a profit and at no burden to the taxpayer.
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