Patrick McLoughlin admitted he sympathised with rail passengers complaining about the trains nicknamed “buses on rails”.
Deputy Prime Minister Nick Clegg has previously said he is pressing for a commitment to scrap Pacers on the northern railway network to be included in the Chancellor’s Autumn Statement and McLoughlin’s comments suggest both sides of the coalition government share that goal.
Speaking during a visit to Calderdale, Mr McLoughlin told The Yorkshire Post: “The simple fact is we are hugely investing in the railways like we haven’t invested in this country for a very very long time so with that comes a lot of electrification, a lot of new rolling stock which is being purchased.
“And I recognise in this area a crying need for people saying, look we are still relying in certain areas on the Pacer which is not the best or most reliable form of transport and I fully accept that.”
He added: “I know that there are certain companies looking at doing some work on the Pacer and improving the Pacer and I would be very interested to see how that comes about and in certain areas the Pacer may provide a service that is relevant.
“But I think there is a case on the more longer distances, I don’t think the Pacer is something I would like to see around in the future.”
A new report from transport research group Greengauge 21, to be published at an event in York tomorrow, will call for the replacement of Pacer trains to be a requirement included in the next transpennine and northern rail franchises.
The Government is due to decide next year which companies will run the two franchises, which cover the bulk of local services in Yorkshire, from 2016 and campaigners want the bidders to set out ambitious plans.
Alongside the phasing out of Pacers, the Greenguage 21 report will urge the Government to use the franchises to create an express rail network for the North and Midlands and a London-style zone system for fares.
The report will be published at an event at the National Railway Museum tomorrow organised by the Campaign for Better Transport.
CBT chief executive Stephen Joseph said: “Northern cities like Liverpool and Leeds have seen major regeneration initiatives recently, and we’re extremely pleased to hear politicians from many parties and local government voice their support for a rail network that makes the most of these economic opportunities.
“But in order for the rhetoric to become reality, the Government and the bidders who win these two key franchises simply must take on board the recommendations of this report, which offers clear, practical steps that need to be taken to give people, businesses and the cities of the region the rail network they deserve.
“Another ‘minimum cost’ franchise, like the previous one, would be a disaster for northern cities.”
Transport campaigners were alarmed by consultation documents on the future of northern rail services published in the summer suggesting a reduction in services might be price that has to be paid for better trains.
But significant investments in transport are now expected to feature in the Autumn Statement after a string of interventions from senior Government figures on the importance of better connections between cities in the North.