Louise Ellman, chairman of the House of Commons Transport Committee and MP for Liverpool Riverside, has raised concerns about the Northern electrification scheme during the first Investing in the Railway inquiry, held on Monday.
Clare Moriarty, director general of the Rail Executive, told the committee that the affordability of electrification was still being assessed and the detailed budget would not be known until March 2015.
Ellman asked Moriarty if the electrification of the transpennine line, part of Network Rail's £38bn investment programme over the next five years, was definitely going to happen.
Moriarty said choices might have to be made if cost overruns were identified and more money needed.
The £100m electrification of the Northern line has been mooted for many years and was unveiled as one of the last Labour government's priority transport projects in July 2009, and confirmed by Coalition Chancellor George Osborne in his autumn 2010 spending review.
The improvement works would reduce journey times between Liverpool, Manchester, Leeds and York.
Ellman told witnesses to the committee she wanted to know if the schemes that had been promised would be delivered.
Ellman asked for more detail on the choices and options if the costs were greater than expected.
She added: "I feel concerned that suddenly all kinds of question marks are being put against this [electrification plan]."
Moriarty said she was not expecting schemes to start and then be abandoned.
Speaking after the inquiry session finished, Mick Cash, acting general secretary of the RMT rail union, said: "This is shocking news. Only last week chancellor George Osborne was parading around talking about a High Speed link in the North and yet today we can't even get a cast iron assurance on the urgent electrification programme in the region that it was assumed would be completed in the next four years. This is further evidence of the continuing shambles on our railways which is down to a combination of sheer ministerial incompetence and the fragmentation of privatisation.
"Coming hot on the heels of the Government's launch of a consultation that would destroy jobs, service and safety on both Northern Rail and Trans Pennine Express this is another hammer blow to rail services in the North and will provoke widespread anger amongst staff and the public alike. RMT will be using this latest betrayal as we step up our campaign to defend rail services and rail jobs."