The UK government has given "a cast-iron commitment" that the electrification of the north Wales main rail line will happen.
Welsh Secretary David TC Davies said the full business case is still to be done but the line will be built.
Welsh ministers dismissed the £1bn cost announced as a "back of a fag packet figure" and a transport expert has put the cost at about £1.5bn or more.
Mr Davies admitted the cost would "probably be a bit higher" than £1bn.
On Thursday, Rishi Sunak announced that £1bn would be provided to electrify the north Wales main line, following his decision to scrap the second leg of the HS2 high speed rail line
Welsh government Economy Minister Vaughan Gething said the £1bn costing was "back of a fag packet stuff".
Speaking on BBC Newsnight, he said no development work had been done into the project.
"If you don't have the development work done then you can't control the costs and they don't really know if a billion pounds will do it," he said.
Prof Stuart Cole, from the University of South Wales and a government adviser on transport, said the prime minister's £1bn figure "presumably includes signalling and straightening the truck".
"However, the figure he used was based on the study in 2015, and construction costs increased by about 7% per annum, so we're now really talking about £1.5bn or more," he said.