Chris Grayling has insisted he is not to blame for the "timetable chaos" which has caused misery for train passengers.
The Transport Secretary said "I don't run the railways" and that industry experts had given the go-ahead for the new timetables.
Shadow transport secretary Andy McDonald said Mr Grayling's refusal to accept responsibility was "evidence that he has lost control" and called for him to quit.
Mr Grayling told BBC Radio 4's Today programme: "The important thing with the timetable chaos, first of all, is to sort things out for passengers."
He said an inquiry would examine how "the industry readiness board, the organisation set up to monitor the arrival of the new timetable, could give this a green light in early May" and how Northern "said they would be ready for the new timetable and they weren't".
Challenged on whether he had overall responsibility, Mr Grayling said: "Actually, no, I don't run the railways.
"And what happened in May is both train companies and the industry experts said 'we will be ready for the timetable change'.
"It didn't happen, that's unacceptable and we need to work out why this went wrong."
Mr Grayling was pressed twice on whether he had considered resigning, but said: "My focus has been on making sure we sort out things for passengers."
Mr McDonald said: "It is remarkable that the Secretary of State for Transport, Chris Grayling, denied that he is the person with overall responsibility for running the railway.
"More evidence that he has lost control and should resign."