Caroline Lucas, the Green MP, has called on the government to strip Govia Thameslink Railway (GTR) of its franchise after allowing it to introduce an emergency timetable for Southern rail that permits the cancellation of 350 trains a day.

The Rail, Maritime and Transport union said it was given the figures at a meeting with officials from GTR, which runs Southern.

Commuters on Southern services have had to endure delays and cancellations for weeks because of staff shortages and strikes amid a row over the role of conductors. The company has blamed high levels of staff sickness for the daily travel chaos.

The RMT general secretary, Mick Cash, has disputed the company’s claims, blaming incompetence: “This latest savage attack on passenger services by GTR is nothing to do with staff sickness and everything to do with gross mismanagement of this franchise and the failure to employ enough guards and drivers to fill the current rosters and diagrams. The solution of this failing, basket-case franchise is not axing more trains and attacking those trying to hold it together at the sharp end – it is the removal of Govia at the earliest possible point.”

Lucas agreed, telling BBC Radio 4’s today show: “The company is incompetent, it should be stripped of the franchise. It should go back into public hands because at the very least we will be able to see all the details. It will be in the public domain, it will be transparent rather than redacted and secretive as it is now.”

The union and company officials will give evidence to MPs on the transport select committee on Tuesday about Southern, which handles the London to Brighton line.

A GTR spokesman said: “We will be confirming details of a temporary timetable tomorrow. The timetable recognises that the present level of service has not been acceptable and will aim to give passengers a more predictable service they can plan around. This will be a temporary measure until train crew availability levels return to normal.”

A Department for Transport spokesman said: “We are aware that GTR is considering some changes in order to strengthen their timetable in the face of ongoing disruption, so as many services as possible can run. When this happens, operators are contractually obliged to inform us in advance, but these decisions are taken only when there is no other solution, and this does not amount to the government giving permission.”

Lucas urged the department to get concerned parties round the table and start “banging heads together” instead of simply “rolling over” and letting more cancellations happen.