Rail passengers on the franchise which provides trains from Huntingdon and St Neots had the worst service performance on the national rail network over the last three years, the National Audit Office (NAO) has said.
The NAO concluded that high levels of disruption for passengers meant the Thameslink, Southern and Great Northern franchise had not delivered value for money.
But Govia Thameslink Railway (GTR), which runs the franchise, may get millions of pounds from the Department for Transport which brought in changes to its contract.
Amyas Morse, head of the NAO, said: "Over the last three years long-suffering passengers on the Thameslink franchise have experienced the worse performance on the rail network.
"Some of the problems could have been avoided if the department had taken more care to consider passengers in its design of the franchise."
The NAO said that after GTR started operating the full franchise in July 2015, around 146,000 services (7.7 per cent) had been cancelled or delayed by over 30 minutes compared with 2.8 per cent on the rest of the network.
Industrial action, mainly on Southern, has been blamed for crew shortages causing cancellations but the NAO there had also been problems with Network Rail's management of the network.
The NAO said the Department for Transport had accepted GTR's plans for 'driver only operation', recognising it would increase the risk of industrial action and the department had not sought sufficient assurances from GTR that it would have enough drivers when it took over the franchise.
The report said the department contracted GTR to deliver a level of increased services despite concerns from Network Rail and GTR that the network could not support the proposed timetables reliably.
The report also said that the department and Network Rail did not have a "good understanding" of the condition of the rail network when the requirements of the franchise were set.
The NAO said that although performance was improving, passengers were continuing to experience disruption. The department had decided not to terminate the contract and a £13.4 million spending programme had been reached with GTR for missing targets.
Charles Horton GTR chief executive, said passengers were increasingly seeing the benefits off an upgrade programme to improve reliability and boost capacity.
"TSGN is the UK's largest franchise, carrying almost a million passengers a day, and the report identifies numerous root causes for the challenges it has faced since its formation in 2014.
"These difficulties have sometimes been greater than expected and we regret the disruption caused to our passengers."