Govia Thameslink Railway (GTR) has not been stripped of its franchise despite its “unacceptable performance” following the introduction of the May timetable.
Transport Secretary Chris Grayling said taking control of services away from the company would “cause further and undue disruption for passengers and is not an appropriate course of action”.
The decision was announced on the day the Transport Select Committee (TSC) published a scathing report which said Mr Grayling should have been more proactive in preventing the chaos that gripped parts of the network earlier this year.
Mr Grayling insisted the Government is “holding GTR to account” by ordering it to pay £15 million for service agreements.
GTR, which is majority-owned by transport group Go-Ahead and runs lines in south-east England including the troubled Southern Railway service, will make no profit this year and will make a reduced profit for the remainder of its franchise until September 2021 as part of the sanctions.
Mick Cash, leader of the Rail, Maritime and Transport (RMT) union, described the punishment as a “half-hearted slap on the wrist for GTR”.
He went on: “By refusing to strip them of the contract, they are being given yet another licence to carry on with chaos by the man who is Britain’s leading specialist in failure.
“Chris Grayling should resign.”
The TSC called for swift reforms to restore passengers’ trust in the railways and said the “chaotic roll-out” of alterations to services across the country should be the catalyst for “genuine change” for people who rely on the network.
The MPs said he was not fully informed of the serious problems caused by the changes, but they added that it was not reasonable for him to absolve himself of all responsibility.
Mr Grayling had the ultimate authority to judge trade-offs between competing commercial interests and he should have been more proactive, said the report.
A Department for Transport spokesperson said: “We have already worked with the industry to deliver special compensation schemes on Northern, TransPennine Express and GTR, which provides the equivalent of up to 8% of the cost of an annual season ticket for those most severely impacted.
“The disruption following the May timetable change demonstrated that significant change is required in the rail industry. That is why we launched the Williams review to consider all parts of the industry in order to put passengers first, with reforms to begin from 2020.”
The TSC found that GTR failed to run about 470 (12%) of its planned 3,880 daily services following the new timetable.
Arriva Rail North, which operates Northern rail services across the North of England, did not run around 310 (11%) of its planned 2,810 services per weekday.
The report said passengers most affected by the delays and cancellations should receive a discount on 2019 tickets.
National rail timetabling needs “genuinely independent” oversight, located outside Network Rail, to avoid being affected by commercial and political pressure, it added.
Last week’s announcement that rail fares would increase by an average of 3.1% added “insult to passengers’ injury”, said Lilian Greenwood, who chairs the committee.
She said: “It is extraordinary, and totally unacceptable, that no-one took charge of the situation and acted to avert the May timetabling crisis.
“Instead of experiencing the benefits of much-needed investment in our railways, around one in five passengers experienced intensely inconvenient and costly disruption to their daily lives.
“There was extraordinary complacency about protecting the interests of passengers, who were very badly let down.
“The complex system by which we operate our rail services failed to cope with the scale of change planned for May.
“The Secretary of State has announced a year-long independent rail review.
“While the need for fundamental reform is beyond doubt, passengers cannot wait until 2020 for key lessons to be learned and reforms implemented.”