Ministers have been accused of scuppering a deal with rail unions and "ensuring misery for millions" of passengers before Christmas.
It comes after Mark Harper repeatedly dodged questions over the controversial issue of driver-only trains in negotiations with unions.
The Transport Secretary refused to say whether the issue had been inserted into negotiations with the rail unions at the eleventh-hour.
His remarks follow the RMT union rejecting an offer from the network operators on Sunday - paving the way for strikes to go ahead next week.
The Telegraph reported the offer made to union chiefs was conditional on accepting driver-only operated trains on the insistence of No10.
Appearing at the Transport Committee on Wednesday, Mr Harper was tackled on the issue by the Labour MP Ben Bradshaw.
"Has the issue of driver-only trains been introduced by Number 10 or the Treasury at the last minute?" he asked. "It wasn't on the table before."
Mr Harper replied: "We're very clear we need to see reform.
"On the specifics about detail, detailed negotiations are taking place between employers and trade unions.
"It's not the Government's role to micromanage the details of the reform."
Pressed again, he added: "No-one is trying to stop a deal - quite the reverse.
"We're trying to reach a deal here, it's the RMT that has rejected, and I think it's regrettable. I'm very clear I want to see a deal reached."
Mr Bradshaw later posted on social media: "Transport Secretary Mark Harper refuses to deny at Transport Committee that the Government inserted the new issue of driver only trains into the rail dispute at the last minute last week, which scuppered a deal, ensuring misery for millions of passengers this Christmas".
Responding the RMT added: "The Tory government is deliberately scuppering any chance of a deal in the rail strikes by inserting last minute DOO proposals that not even the train operators wanted".
During the grilling from MPs on Wednesday, Mr Harper also urged union leaders to "call off" the pre-Christmas strikes.
As it stands RMT's members will strike on December 13, 14, 16 and 17 while those who maintain the tracks will down tools between 6pm on Christmas Eve until 6am on Boxing Day.
Mr Harper said: "I would still urge the unions to keep talking, put those deals to their members with at least a neutral recommendation, and call off the strikes before Christmas which are going to be so damaging to individuals and businesses across a whole range of sectors.
"The Government will do what we can to try and encourage both employers and unions to keep talking."
