The new transport secretary has been urged to take action over Govia Thameslink Railway’s “rock bottom” punctuality ratings a week after the rail operator axed hundreds of trains to ease disruption.

The Rail, Maritime and Transport (RMT) union has demanded an urgent meeting with Chris Grayling, who was appointed to the role by Prime Minister Theresa May Thursday, to address what it claimed was “gross mismanagement” of the company.

Govia cut 341 trains a day from its Southern franchise’s timetable on Monday last week in a move it claimed would offer “greater certainty for commuters”.

Despite the introduction of the temporary “emergency” timetable, 38 per cent of Southern trains ran late on Sunday.

Only 51 per cent of trains across Govia’s franchises, which also include Great Northern and Thameslink, arrived on time, with 73 per cent reaching their final destination with five minutes of their scheduled arrival time.

Southern blames high levels of staff sickness as well as industrial action by the RMT in a dispute over the role of conductors.

Mick Cash, RMT general secretary, said: “[Chris Grayling] said that he wants to address the crisis on Southern as a priority and the idea that he can do that without taking full account of the views of our members working at the sharp end of this failing franchise is untenable.

“If the politicians continue to try and blame the staff for the failings on these routes it will be a massive missed opportunity that lets GTR off the hook yet again.

“The real problems on Govia Thameslink remain gross mismanagement, a chronic shortage of fleet and capacity and a failure to recruit enough staff to fill the rosters and diagrams.

“Those problems are compounded by a drive to undermine and attack the safety-critical staff who are crucial to the running of the railway.

“It is those issues that the new transport team must be forced to address.”

Southern reinstated 16 trains to its emergency timetable following a furious backlash from commuters last week.

Last week more than 100 angry passengers staged a protest at London Victoria station following months of frequent cancellations and disruptions to the service.

A Department for Transport spokeswoman said: “The current situation with Southern is unacceptable and passengers deserve a far better service.

“We have been clear that the real solution is for the RMT to bring this dispute to a close and end the high levels of sickness absence amongst its members.

“Improving the situation is and will remain a priority until this issue is resolved.”

Alex Foulds, Southern’s passenger service director, said: “Although we are running fewer trains, we are providing greater certainty for commuters by concentrating our resources on providing a more reliable and punctual rush hour service.”

The operator has been heavily criticised by MPs, some of whom have called for it to be stripped of its franchise, and slammed by passengers, who named the company as the worst in the country in a passenger survey published last month.

On Friday rail minister Claire Perry stepped down from her position, telling Parliament she was “falling on my sword” over Southern’s failures.