Sir Clive Betts said journey times between Sheffield and London had already been lengthened to accommodate more commuter trains on Govia Thameslink (GTR) lines servicing the capital.
And now Stagecoach, which operates the Midland Midland Main Line, is being told by the DfT that it cannot look to improve journey times from South Yorkshire to London in the next set of timetable changes because officials are nervous of another “shambles”.
At transport questions in the Commons, the Labour MP for Sheffield South East said: “On the last timetable changes Midland Main Line (run by) Stagecoach were forced to lengthen the journey times of the peak time train from Sheffield to London to accommodate more commuter trains on Thameslink.
“Is it true now that the Department for Transport has told Stagecoach they can’t come and revisit that in the next timetable changes because of the shambles last time and the nervousness that’s created in the department?”
Transport Secretary Mr Grayling replied: “We would dispute that we have done anything to disadvantage Sheffield to help GTR.
“We are of course doing a massive upgrade programme on the Midland Main Line at the moment and I would pay tribute to all of those involved in the recent Derby station remodelling, there have been many projects that have gone badly wrong and that did not and was handled very well.
“Of course there are further improvements happening up and down that line.”
He added: “That work will continue, we will do everything we can do to make sure, if we can, the timetable remains as intact as possible as those changes happen.”
Meanwhile, Mr Grayling denied accusations that he has a "tin ear" after he was criticised over a lack of investment in railways in the North.
It came after an IPPR North analysis showed earlier this week that public spending on transport in Yorkshire and Humber fell by Â£18 per person last year while increasing Â£90 in London.
Mr Grayling insisted he was "actively working to try and improve things", amid questions from a former Shadow Transport Secretary on the reliability of northern train services.
Wakefield MP Mary Creagh accused Mr Grayling of "showing a bit of a tin ear to the lived experience" of her constituents.
"One of whom took six hours to travel the 75 miles between Wakefield and Scarborough - a feat that with a good wind I could have achieved on a bicycle in the same amount of time," the Labour MP said.
"Can he tell us why the IPPR is showing that capital investment in the North has fallen at a time when the need for investment in our services has never been higher?"
But Mr Grayling said it was "not a question of having a tin ear", telling the Wakefield MP the network was delivering "more services rather than fewer".
The Tory Minister said: "In the North, in her own area, the flagship programme for the next five years on rail TransPennine upgrade is the most substantial anywhere in the country.
"Her constituency is also benefiting from increased services on the route to Knottingley - I do accept that there have been some real issues with TransPennine Express on the route to Scarborough - those are things that need to be addressed, there are performance issues that are not good enough.
"So it's not a question of having a tin ear - we are actively working to try and improve things on a network that is delivering more services rather than fewer and in which there is substantial investment happening."
Later, Tory former Minister Sir Desmond Swayne said it must be "ghastly to be the Rail Minister".
Referencing the resignation of former Rail Minister Jo Johnson over Brexit, he asked: "Does he think that it might have contributed to his predecessor's resignation?"
Newly-appointed Transport Minister and Harrogate MP Andrew Jones replied: "That question is flawed - there is nothing ghastly at all about being the Rail Minister and I can't understand where he is coming from on that question.
"As regards the reasons for my predecessor's departure, I think they are already documented elsewhere."