Ministers are considering taking direct control of the rail franchise that includes Southern rail, it has been claimed.

Options ranging from splitting off Southern from Govia Thameslink Railway (GTR), to a complete “managed exit” to take direct control of the entire franchise until a new contract could be let are under consideration by the Department of Transport, according to the Rail Business Intelligence magazine.

Passengers on the blighted route have finally seen a full timetable restored, with the suspension of strikes while GTR holds talks with the train drivers’ union Aslef, but the department is still adjudicating on a question of whether the company breached the terms of its franchise.

Commuters have suffered almost two years of disruption and delay on the rail network, a situation that has been exacerbated by strikes since last April. GTR claimed in 2016 that its failure to run adequate services was down to force majeure – the effects of industrial action – but the department has yet to confirm whether it is in breach of contract, despite months of review.

The department said it was still considering the question of whether GTR was in breach of its franchise commitments, despite months of pressing on the issue from the transport select committee.

The rail minister Paul Maynard recently wrote to the chair of the transport select committee, Louise Ellman, stressing that even if GTR’s claim of force majeure was rejected and the firm was found to be in breach, it would not necessarily lose the contract.

Ellman said the latest reported moves showed the department is in an “increasing desperate situation”. She added: “Commuters are angry, the government’s own MPs are angry, and the transport committee can’t even get a straight answer on force majeure.

“In the meantime GTR are picking up billion pounds a year, and the cost to the public purse from lost revenue is £38m – the government must take a decision. How ever unpalatable, they can’t let this continue.”

Any direct control or hint of re-nationalisation would be anathema to the transport secretary, Chris Grayling, who has repeatedly stressed that there is no better alternative than GTR. The government’s in-house operating company of last resort, Directly Operated Railways, which ran East Coast for six years when National Express walked away from the franchise in 2009, has been disbanded. Engineering firm Arup and consultants EY have a contract to help establish stand-in, emergency franchises.

A spokesman for the transport department said there were no plans to strip GTR of its franchise, describing the report as “pure speculation”, while a GTR spokeswoman said: “The article is just speculation and we wouldn’t comment on it. As you would expect there are always discussions with the DfT regarding the GTR franchise contract and our other franchise contracts.”

Meanwhile, talks are continuing between Aslef and Southern to try to resolve their row over driver-only trains. Planned strikes were suspended after talks started a week ago, but neither side has commented on whether any progress is being made.

A small number of members of the RMT union at Southern went on strike on Wednesday and will walk out again on Friday.

The RMT general secretary, Mick Cash, said: “Instead of dragging this farce out any longer the government should now do the decent thing, pull the plug on the GTR contract, take the lines under public control and draw a line under this shambles that shames Britain’s railways.”