Transport Secretary Chris Grayling has sought to dismiss fears of a "bias" against northern regions over rail spending.
The Cabinet minister labelled the description of the Government's commitment to projects in the North as a "total misnomer" before arguing that spending will be higher per head of population than in the South.
The Government has been accused of "reneging" on commitments after failing to confirm plans to fully electrify the Manchester to Leeds route.
Timetable chaos has also caused major disruption for Northern rail passengers.
Speaking in the Commons, Labour's Judith Cummins (Bradford South) said: "In recent weeks we've seen endless delays, cancellations across the North and a report from the Transport Select Committee which confirms there is a bias against northern regions in rail investment decisions.
"And now there are reports that Transpennine electrification is going to be scrapped altogether.
"Will the minister now respond properly to the One North campaign and commit to giving Transport for the North the full powers and funding it needs to deliver the changes we need?"
Mr Grayling replied: "I'm afraid this is a total misnomer.
"Firstly, the part of the country over the next five years receiving the highest transport spending per head of population from the Government is actually the North West, and across the North the spending is higher than it is per head of population in the South.
"We will start, as I've already announced, next spring the £3 billion Transpennine upgrade, which will substantially rebuild the railway line between Leeds and Manchester and York, and deliver much better services to passengers. Long overdue."
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