The project will come under the spotlight tonight in a Channel 4 Dispatches programme called The Great Train Robbery.
Senior ministers have told the show that the link might only ever go as far as Birmingham as a poll revealed commuters want cash focused on Northern Powerhouse rail projects to ease overcrowding.
Dispatches will air claims that over the next decade HS2 will cost up to £6bn a year – equal to the entire network annual maintenance budget.
The programme also claims the final cost could top £100bn.
Mark Thurston, CEO of HS2 said he was confident the scheme will be built on budget.
He said: “When High Speed 2 and the work of Northern Powerhouse Rail all brings together an intergrated rail network to connect those northern cities it will transform the northern economy.
“What we are very clear on is the budget for this scheme is £56bn and we have to build this railway for £56bn.”