Both Sheffield and Leeds are on the Government’s flagship high speed rail link, however concerns have been raised in both cities over where passengers will get off.
Patrick McLoughlin MP told the Yorkshire Post how cost was the most important factor in any new proposals.
The chair of HS2, Sir David Higgins, is due to report back on where the location of the Leeds station should be - either within the existing train station or in the city’s South Bank area.
Mr McLoughlin, said: “We are waiting for the David Higgins report on that. It’s absolutely right we get that in conjunction with what the local council does.
“Now Queens station at the moment is an incredibly busy station. It is constrained by where it is, but David Higgins’ report will be published and we will have the results by the end of this year so not too far to wait.
“I hope it gives the answers and the investment as far as Leeds is concerned.”
Mr McLoughlin referred to Leeds’ train station as ‘Queens’ due to its location next to The Queens hotel.
In Sheffield, the HS2 station is planned to be built near Meadowhall shopping centre, just outside the city and £1bn cheaper to construct, however there has been a push for it to come closer to the city at the former Victoria Station for maximum economic benefit.
He said: “As far as Sheffield is concerned they are making the case for Victoria to reopen, as opposed to the Meadowhall station.
“These do cost huge amounts of money and we do have to look at value for money as far as they are concerned.”
In a speech to the party conference today Mr McLoughlin will outline how twenty years ago 750 million railway journeys were made a year, which has now risen to 1.6bn journeys a year.
He said neither David Cameron nor George Osborne have ever needed convincing on rail investment, and the Chancellor today is launching a new Infrastructure Commission, which will look at connections between Manchester and Leeds.
He said the winner of the new Northern Rail franchise, which will be announced in December, would be taking over a route that changes travel between northern cities but he was unable to rule out the use of driver-only trains that have attracted so much criticism from the union of Rail, Maritime and Transport Workers.
The union believes they are a serious threat to jobs.
Mr McLoughlin said: “I can’t discuss what’s going to be in the new franchise.
“I just wish the RMT would be a bit more positive about what’s happening to their industry. It’s a great pity that the RMT will always look on the black and negative side of life.
“There’s more people employed in the industry now than there has been in 30 years. “There’s more people using the trains, they are much more important to society.
“I think the RMT should be blowing the trumpet of the railways instead of continually whinging.
“The levels of investment in our railways are of the like we’ve not seen before and we certainly didn’t see between 1997 and 2010 when we saw 10 miles of electrification of the railways network, as opposed to the 800 miles we’ve got planned over the next five years.”