Rail passengers and taxpayers are paying the price of costly mismanagement of the railways by the Department for Transport, according to a scathing report.

The public accounts committee warned that more problems lie ahead for train users in 2019 after a “year from hell”, marked in particular by the chaos following the introduction of a new timetable in May.

It lambasted the DfT for issues including breaking promises on new services; secrecy over contracts; its handling of major projects and disruption; letting down disabled passengers; and general management of the railway.

Labour said the report, from the cross-party Commons committee, was “damning of the utter incompetence” of the DfT and Chris Grayling, the secretary of state.

Grayling announced a full rail review, chaired by the former British Airways boss Keith Williams, after the mounting problems last year.

Williams told an industry gathering on Tuesday night that the rail franchising system had to change. In the George Bradshaw address, Williams said: “Put bluntly, franchising cannot continue the way it is today. It is no longer delivering clear benefits for either taxpayers and farepayers.”

The PAC report said the DfT’s management was still characterised by cost overruns, project delays and disruption, with another year of further significant timetable changes, maintenance and engineering work coming up.

Addressing the timetable chaos, the committee said: “Given the fragmented nature of responsibilities for operating the railway, it is alarming that the department has not ensured a clear line of ownership and oversight of the timetabling process, and that it did not sufficiently probe the assurances it was getting from industry on progress.”

It said the DfT was “still not adequately protecting taxpayers’ money” with regard to the biggest commuter franchise, Govia Thameslink Railway, where passengers have experienced the worst performance nationally over the last few years, and there was not enough transparency over its finances.

It accused the DfT of failing to learn lessons, citing Crossrail, the delayed train line through London whose problems were announced months before the planned opening last December. The PAC said the DfT again “did not sufficiently probe the assurances given by Crossrail over the progress of the programme and its expected cost”.

The MPs demanded that the DfT set out exactly if and when direct services to towns and cities such as Huddersfield, Sunderland and Middlesbrough that were promised when it awarded the East Coast franchise in 2014 will appear.

The report concluded that the DfT and rail industry had been too slow to act to make the railway accessible for passengers with disabilities.

Meg Hillier, the PAC chair, said: “2018 was a year from hell for many rail users and unless the government gets a grip there is every chance that passengers will suffer in 2019 as well. Crucially, the Department for Transport did not ensure that those responsible for the railway were clear about their roles and were working together effectively.”

Labour’s shadow transport secretary, Andy McDonald, said the report was “damning of the utter incompetence of the DfT and its ministers” at a time when fares continued to rise.

He added: “Chris Grayling has failed to provide leadership, throwing the railway into chaos and wasting hundreds of millions of pounds of public money.”

The PAC report follows the interim inquiry into 2018’s timetable chaos, led by the outgoing Office of Rail and Road chairman, Stephen Glaister, which found that “no one took charge” of the changeover even as it became apparent the industry could not deliver.

A DfT spokesperson said the lessons of the Glaister report had helped it to deliver timetable changes in 2018, adding: “The independently chaired root-and-branch review of our railway is considering all parts of the rail industry to ensure the focus is on putting passengers first. The government and rail industry are committed to working together to ensure improvements are made.”