The Government will defy "grief and hassle" from its own backbenchers and fast-track plans for a new high-speed rail link between London and Birmingham, the Transport Secretary has told The Independent.

Patrick McLoughlin dismissed suggestions that the Department for Transport's financial modelling errors behind last week's West Coast Main Line debacle would undermine High Speed Two. The project had the unequivocal backing of both David Cameron and the Chancellor, George Osborne, he added.

Mr McLoughlin also indicated that there would be no significant compromises on the published HS2 route between London and Birmingham despite vocal opposition from the Conservative MPs through whose constituencies the line will run.

"The easiest thing for any government to do on a project the size of HS2 is to say we're not doing it," he said. "All we get is grief. All we get is hassle. But one of the things that government has got to try and do is to look to the long-term future.

"Whichever route we're going to put it on we're going to upset people."

Mr McLoughlin said he would "love to" complete the project within five years but admitted that it would almost certainly take longer.

However he is expected to bring forward the legislation needed to start work on the line in the next Queen's Speech and said he was prepared to work with Labour to get HS2 through Parliament before the next election. He will also publish a route for the next stage of high-speed rail in the next few months which will eventually link London and Manchester.

There had been speculation before the reshuffle that the Government would put HS2 on ice in the face of strident opposition from protesters along the planned route – many of whom live in Conservative-held seats.

Mr Osborne was said to have cooled on the project which was described as "effectively dead". But Mr McLoughlin said when he was appointed in the reshuffle it was made very clear to him that the project had the full support of both Mr Cameron and Mr Osborne.

"The Chancellor is committed to it," he said. "The Chancellor is determined that it goes to the North."

Mr McLoughlin said critics of the project – who argue that the shorter journey times on HS2 were not significant enough to justify the cost and destruction to the countryside – were missing the point.

"There has been a huge change in the way we look at transport since the Birmingham-to-London line was built almost 200 years ago," he said.

"At one stage it looked like the age of the train was dead. But the age of the train is not dead."

In a move that will infuriate his Tory opponents Mr McLoughlin said he was even prepared to work with Labour to ensure the legislation necessary to start construction was not bogged down in Parliament.