Profits were slashed at Transpennine Express during its latest financial year despite the train operator receiving almost £260m from the government.
Newly-filed accounts with Companies House have revealed the firm's pre-tax profits slumped from £72.1m to £8m in the 12 months to March 31, 2022.
Transpennine Express received a revenue subsidy from the Department for Transport of £259.3m, down from £325m.
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The operator said the decrease in its overall turnover from £437.7m to £420.9m due to the prior year's total including exceptional income of £59.9m.
Transpennine Express operates services to the likes of Liverpool, Manchester, Leeds, York, Newcastle, Sheffield, Hull, Middlesbrough, Scarborough, Cleethorpes, Preston, Carlisle, Glasgow and Edinburgh.
During the year passenger receipts surged from £45.5m to £151.9m having fallen by more than 80% in the prior 12 months.
Transpennine Express, along with Northern Trains and Avanti West Coast, has come under fire in recent months over delayed and cancelled services.
Rail bosses were questioned by MPs in December 2022 while questions have been raised recently about whether the number of services cancelled by Transpennine Express are being 'masked'.
Last month, BusinessLive reported that Northern would have made a loss of more than £600m if it had not received Government support during its latest financial year.
A statement signed off by the board said: "During the year, passenger volumes increased following the easing of travel restrictions in England from spring 2021 and again in February 2022.
"In the leisure market, volumes have recovered particularly well, with demand on some flows higher than before the pandemic.
"We continue to work closely with the DfT on appropriate service provision, with services being altered during the year to reflect pandemic and other impacts.
"The company has experienced some temporary shortages of employees during the year, resulting from increased sickness and self-isolation, but this did not materially impact the company's overall financial performance.
"Traincrew availability in the latter third of the year was also challenges by the loss of rest day working by drivers and the National Union of Rail, Maritime and Transport (RMT) industrial action by its conductor members at TPE.
"Despite these issues, which impacted service performance and revenue in the latter part of the financial year, the company delivered overall passenger and other performance metrics in line with expectations with the accounts based on management's estimate of fees receivable.
"TPE has generated satisfactory returns despite challenging industry conditions and is focused on working with its industry partners to deliver better customer experiences, which will in turn result in passengers returning to the railway.
"We continue to work closely with Network Rail, the DfT, industry partners and mayoral, combined and local authorities to deliver [Transpennine Route Upgrade] TRU and other projects while minimising planned disruption for passengers."
The accounts come as new figures revealed that complaints about train operators Avanti West Coast and TransPennine Express soared as performance deteriorated.
Office of Rail and Road (ORR) data revealed that 238.6 complaints were made per 100,000 journeys on Avanti West Coast between July and September last year, up 51.3% from a year earlier.
TransPennine Express saw an even larger percentage increase, up 65.4% to 76.9 complaints per 100,000 journeys.
Both operators’ services were hit by widespread delays and cancellations over that period, partly due to a sharp decline in the number of drivers voluntarily working on rest days for extra pay.
The proportion of trains that arrived at stations within one minute of the schedule between July and September fell year-on-year by 17.0% for Avanti West Coast and 10.2% for TransPennine Express.
The companies reduced their timetables to reduce short-notice cancellations.
Across all train companies in Britain the rate of complaints between July and September was 24.0 per 100,000 journeys. That was down from 29.3 a year earlier. The total number of complaints for the quarter reached 86,385.
This was a rise of 18.8% from the same three months in 2021, coinciding with a 44.9% increase in journeys.
An Avanti West Coast spokesman said: “We know that last summer our customers were not getting the service they deserved and these figures reflect an extremely challenging time.
“We are sorry for the enormous amount of frustration and inconvenience this caused and we’re grateful for the patience our passengers have shown.
“Over the last few months, our sole focus has been to do everything we can to return to a more resilient operation which delivers more services for our customers and communities.
“Our new timetable introduced in December has greatly increased the number of services we run and customers are now seeing the benefits of that, with more trains, greater connectivity and tickets on sale much earlier.”
A spokeswoman for TransPennine Express said: “It is always disappointing to hear or read that any of our customers experience circumstances which lead to a complaint, but we accept that the service we have provided recently has fallen well short of what our customers expect and deserve and we are sorry for the disruption to journeys.
“The period covered by the ORR data was particularly difficult as we were experiencing ongoing disruption caused by sickness and the driver training backlog, as well as localised strike action by RMT members prior to the national dispute.”
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