A train company at the centre of a bitter dispute over staffing is being allowed by the Government to make thousands more cancellations under an amendment to its franchise, a leading union has claimed.

A so-called "remedial plan" between Govia Thameslink Railway and the Government was agreed earlier this year and "smuggled out" under a raft of documents on the last day of Parliament yesterday, according to the Rail, Maritime and Transport union.

Under the new contract, Southern Railway will be allowed to increase cancellations by a third to 32,000 a year, the union claimed.

Southern said the new targets reflect what is now understood as the limitations on the network during improvement works at London Bridge.

The company is in dispute with the RMT over the role of conductors, which has led to industrial action.

Southern has also reported a big increase in the number of staff taking time off sick, which has led to a series of cancellations, although this has been disputed by the union.

The RMT said the remedial plan admitted that the use of driver-only trains had "significantly increased" the number of incidents leading to delays and cancellations.

The union accused Transport Secretary Patrick McLoughlin of ordering 25 redactions, mostly relating to staffing issues, from the 20-page document.

RMT general secretary Mick Cash said: "The dirty secrets of rail franchising are dragged out under the spotlight in this heavily-redacted document which will send shock waves through the rail industry and which will also spark a new wave of anger amongst the passengers on the GTR franchise who are caught in the middle of this scandal.

"Not only are the Government bending the rules, and inflicting more misery on the travelling public, but they are admitting that driver-only operation, the issue at the heart of the current Southern dispute, has already compromised safety and led to a spate of cancellations.

"The Government are now opening the door to GTR to hack back and cancel services at will without fear of any penalty."

A Govia spokesman said: "The revised benchmarks are designed to be challenging but attainable. What has now been established is that the assumptions around the capability of the network did not recognise the effects of the works at London Bridge and the Thameslink Programme.

"The plan accepts an independent study that 'clearly shows' there has been a structural change in the operating characteristics of the rail network which has affected the level of delay across our network including the level of delays we cause.

"In accordance with the contract provisions, the benchmarks have therefore been adjusted to reflect the reduced capability of the infrastructure."

A GTR spokesman added: "The RMT is deliberately twisting and exaggerating the facts. We know it's been tough for our passengers and this plan highlights the initiatives we're taking to give them a better, more reliable service so that fewer services - not more - have to be cancelled than are today.

"The remedial plan contains our commitment to make a considerable investment over and above our franchise agreement in the areas of driver recruitment and training, rolling stock reliability and performance improvement.

"Our experience of running both Driver Only Operation (DOO) and non-DOO trains shows us that DOO offers higher levels of reliability in train services as they don't have to be cancelled if a conductor is not available.

"The RMT has deliberately taken out of context a comment about normal teething problems that had been experienced during the introduction of one of our new fleets of trains. The same section of the plan goes on to so say 'the underlying reliability of the Class 387/1 fleet is strong and is improving'."

A Department for Transport spokesman said: "Passengers have had to put up with unacceptable levels of cancellations on the GTR network, and it is right that the operator is taking robust, positive steps that will ensure fewer services are cancelled, not more. These targets are both challenging and realistically achievable.

"Improvements won't happen overnight, but the Remedial Plan sets out clear long-term improvements including recruiting and training more drivers, and introducing more reliable trains on the line.

"Some of these changes are already being delivered and we continue to work with GTR to ensure they deliver the high-quality service that passengers deserve."