|The first phase of Crossrail is due to be fully operational in 2019|
Chris Grayling has pledged to work with London mayor Sadiq Khan to ensure Crossrail 2, the multibillion north-south rail line running across the capital between Hertfordshire and Surrey, was "fair to the UK taxpayer".
But Greater Manchester mayor Andy Burnham said people in the region have had to put up with "sub-standard" rail services for decades and would "simply not accept" that spending billions more on transport in London was the "highest priority".
And Liverpool City Region mayor Steve Rotheram also queried the announcements, saying that while he did not "begrudge" the investment in Crossrail 2, there needed to be balanced spending to "support growth in the North as well".
|Mr Grayling warned 'we have to ensure that we get this right' given the price of Crossrail 2|
Mr Grayling was criticised last week for scrapping the long-awaited rail electrification plans on the main lines from Cardiff to Swansea and Kettering to Sheffield.
On Monday it was revealed that Mr Grayling and Mr Khan had agreed on the need for new infrastructure in the capital during a meeting last week, as well as a funding package which "works for both London and the rest of the country".
Mr Grayling said he was a "supporter" of Crossrail 2, but warned that "we have to ensure that we get this right" given the price tag.
|Mr Burnham has said he wants to challenge the Government's 'neglect'|
"It raises the question of whether taxpayers everywhere else outside of London are paying to make Crossrail 2 viable."
Mr Burnham added: "The time has passed where we can take these decisions lying down.
"I will today be contacting fellow metro mayors and council leaders across the North of England to consider how we best challenge this Government's continued neglect of transport in the North together."
Mr Khan and Mr Grayling agreed on the need for new infrastructure in the capital
Mr Rotheram said: "Sadly the juxtaposition of last week's cancellation of northern rail electrification schemes and this week's green light for Crossrail, suggests it is just going to be business as usual from this Government when it comes to transport investment."
The Department for Transport said plans to electrify the Transpennine route have not been scrapped.
A spokesman said major upgrades to the Manchester - Leeds - York route were currently being "designed and developed, to enable us to deliver better journeys for passengers from 2022".
He added: "Passengers expect high quality rail services and we are committed to electrification where it delivers benefits, but will also take advantage of new technology to improve journeys."
The spokesman added that it has not yet been decided whether the entire line will be electrified, and an investment decision will be made next year.
An analysis by the independent think-tank IPPR North found the North of England would have got £59bn more over the last decade, had it received the same infrastructure spending per person as London.