A total of 5.2 per cent of Elizabeth line trains were cancelled between July and September, according to latest figures from Office for Rail and Road.
With 91,122 Elizabeth line trains having been planned, this means that about 4,740 will have failed to run, either in full or in part, over the late summer period.
The line also suffered a 4.5 point annual fall in punctuality, with 82.8 per cent of trains arriving on time or within five minutes of timetable.
However, this was the second best performance of all UK train firms and came as it tried to increase the number of trains by 15 per cent with the “through running” of services from one end of the line to the other.
The line, which opened in May 2022 and which links Shenfield and Abbey Wood with Heathrow and Reading, was badly hit by a major Network Rail signalling failure west of Paddington on July 25 and 26 and a train fault at Paddington on August 26.
Greater Anglia remained the country’s most reliable railway, with 87.2 per cent of trains arriving on time.
Across the UK rail network, 86.9 per cent of trains arrived on time or within five or 10 minutes, depending on each line’s individual target under the “PPM” (public performance measure) figure.
A total of 3.5 per cent of services were cancelled. Three in five cancellations were blamed on train firms, the ORR said.
Only 74.7 per cent of London Overground trains arrived on time, meaning it fell from fourth to sixth place in the national league table for punctuality. Chiltern, C2C and Caledonian Sleeper took the third, fourth and fifth places.
A TfL spokesperson said: “The Elizabeth line has been one of the most popular and punctual railways in the country since opening.
"There are around 4.3 million passenger journeys now taking place each week and there have been more than 270 million journeys since it was opened, but we sincerely apologise for the disruption that has affected some Elizabeth line services in recent months and we recognise that delays and cancellations are frustrating for our customers.
“From July to August 2023, the Elizabeth line had the second best punctuality in the country, and although cancellations are higher than we would like and higher than the same period in 2022, we increased services in both November 2022 and May 2023, providing extra, more direct services for our customers.
“We are working with Network Rail and Alstom, which maintains the trains, to minimise the impact that faults have on the Elizabeth line.
"Recent signalling and infrastructure issues on Network Rail track in the west has had a significant impact on reliability, as have other issues such as trespassers on the line. We will continue to do all we can to drive down delays so we can provide our customers a safe and reliable railway.”
The ORR said the figures, published on Thursday, showed Britain’s railway was “still not delivering consistently punctual and reliable journeys”, with only 69.2 per cent arriving bang on time.
Feras Alshaker, ORR director of planning and performance said: “As the independent regulator, the data we are publishing today bears out the reality that passengers in some areas are still experiencing trains not consistently arriving on time, and high levels of cancellations. However, we are beginning to see signs of improvement in Network Rail’s contribution.
“While these improvements are promising, they aren’t consistent, and as our analysis shows, the company can do much more to ensure that Britain’s railway provides a reliable and punctual service for all its users.
“We recognise that ensuring trains run as planned and to time requires cross-industry collaboration. Network Rail can play an essential part in bringing the rail industry together to build on recent performance improvements and we will work with government to strengthen these relationships.”