It comes just months after the new line, which links Reading and Essex via central London, opened on May 24.
A total of 9.1 per cent of services on the Elizabeth line did not run in the four weeks to August 19, an increase from 3.3 to 3.9 per cent compared with the previous four weeks.
Last week, it was revealed almost half of trains arrived at least a minute late.
According to Transport for London (TfL), up to 24 trains an hour are expected to run at the busiest times between Paddington and Whitechapel.
But commuters have complained about numerous disrupted journeys on the line since its opening.
Elizabeth line director Howard Smith apologised for a “difficult period which included disruption for our customers”.
“There were a number of recent issues including significant problems with Network Rail’s signalling systems and infrastructure on the western section, and a defective maintenance train,” Mr Smith said.
“We continue to work with all parties involved in the Elizabeth line to provide a safe and reliable railway.
“This includes our partners, such as Network Rail, and a programme of upgrades delivered by the train manufacturer, Alstom, will further improve reliability of our fleet of trains.”
There was a Network Rail signalling system outage from July 25 that last two days on the western section of the route, which severely impacted Elizabeth line services.
On August 16, there was another incident where a maintenance train leaked hydraulic fluid within the central tunnel section of the Elizabeth line.
The fluid had to be cleaned from more than 2km of track and the Elizabeth line was part suspended.
A review has already resulted in changes to maintenance practices and to incident management, TfL said.
In July TfL revealed that the Elizabeth line is responsible for 140,000 “new” journeys in the capital each day.
The £20bn line is attracting thousands of passengers from the Tube – with more than a third of those switching from the Underground preferring it to the Central line.
Since May the Elizabeth line has carried more than 200 million passengers, with around 4.1 million passenger journeys now taking place each week.
Meanwhile the first Elizabeth line stations to get super-fast 4G smartphone connectivity were named on Friday - alongside a pledge to have all its central London stations connected by next Spring.
Bond Street, Tottenham Court Road, Farringdon and Liverpool Street stations will join Transport for London’s high-speed mobile data network by Christmas.
The line’s seven other stations and tunnels between Paddington, Abbey Wood and Stratford will be completed by the end of April.