Taxpayers face paying more to ensure new trains for the railway which links Yorkshire to London and Edinburgh work properly.
It emerged yesterday that the Azuma trains due to run on the East Coast Main Line by the end of this year cause electromagnetic interference to older signals and points north of Colton Junction, near York.
It means the electro-diesel trains can only run on diesel and therefore travel more slowly than the speed promised on affected sections of track.
The revelation appeared to spark a dispute between publicly-owned infrastructure operator Network Rail and Japanese train manufacturer Hitachi.
Network Rail said it felt Hitachi was responsible for fixing the problem, but admitted it will have to update line side infrastructure so the trains could run.
But Hitachi appeared to suggest Network Rail was responsible for updating 30-year old signalling systems so the trains can operate on the line.
“This is the same issue encountered 15 years ago when the Pendolino was introduced on the West Coast Mainline,” a spokesman said.
“Whilst testing started over 12 months ago, this issue has been identified by Network Rail only recently during multi-train testing.”
Former Transport Secretary Lord Adonis told The Yorkshire Post: “I ordered these trains 10 years ago and it is incredible that in this time they have not sorted out power issues so they can run properly.
“This is yet another failure by Chris Grayling and his Transport department, for which travellers in Yorkshire and the North are paying dear.”
Shadow Transport Secretary Andy McDonald said the procurement process for the trains had been “incompetently managed” by the Department for Transport, arguing it has cost taxpayers “hundreds of millions of pounds”.
He added: “Once again, the Transport Secretary has failed to ensure that the different parts of the rail industry work together to deliver new infrastructure and services.”
Mr Grayling told BBC One’s Inside Out there were “teething problems”.
The new trains are being assembled by Hitachi Rail in Newton Aycliffe and Country Durham, and are supposed to deliver faster, more reliable and more environmentally friendly trains with more seats and more frequent services.
They are due to be introduced by the end of the year and are currently being tested.