Two thirds of multi-academy trusts (MATs) have Progress 8 scores below the national average, according to new government tables that rank their performance.
The tables compare the performance of 47 MATs at Key Stage Four, and 95 at Key Stage Two.
A government commentary said that the number of MATs performing below average at Key Stage Four does not take account of the historic poor performance of schools that became sponsored academies.
It found that 11 MATs (23.4 per cent) "were performing above the national average by a statistically significant amount", while 24 (51.1 per cent) were performing below the national average by a statistically significant amount.
The analysis will raise concerns about the how well MATs are serving their disadvantaged pupils.
It said: "A relatively high proportion of MATs with higher percentages of disadvantaged pupils are performing statistically significantly below average.
"Nevertheless, there are still six MATs with relatively high proportions of disadvantaged pupils that are performing statistically significantly above average."
At Key Stage Two, more than half of MATs had above average progress in writing and maths, but half were below average for reading.
When MATs with a larger proportion of disadvantaged pupils were considered, eight "performed above the average by a statistically significant amount" for reading progress, and 20 were below average.
In contrast, a "relatively substantial proportion" of MATs with higher numbers of disadvantaged pupils "are performing above average by a statistically significant amount" for progress in maths and writing.
The figures also showed that "some MATs" which are solely made up of sponsored academies "do have relatively low educational performance scores", although there were others that were performing strongly.
The tables include trusts that have at least three schools that have been with them for three years or more.
Best and worst performers
The table compares the performance of 47 multi-academy trusts (MATs) on their 2015-16 performance on the new Progress 8 measure for Key Stage Four.
A total of 11 MATs are rated "significantly above average", with the top performer named as the City of London Corporation, which has three secondary schools, on +0.63, against the average score of 0.
It was followed by the Diocese of London (+0.43), Harris Federation (+0.42), Outwood Grange Academies Trust (+0.41) and Cambridge Meridian Academies Trust (CMAT) (+0.32).
The Hart Schools Trust, which is centred on Hertfordshire and Bedfordshire and has three schools included in the measure, was named the worst performer, with a score of -1.17.
Other MATs joining it at the bottom of the table were the Midland Academies Trust, Northern Education Trust, Greenwood Academies Trust, and the Education Fellowship Trust.
For Key Stage Two, the data compares the progress measures for reading, writing and maths of 95 MATs.
For reading progress, the Wolverhampton-based Central Learning Partnership Trust, which has three primary schools included in its scores, topped the table.
It was followed by South Nottingham Catholic Academy Trust, St Barnabas Catholic Academy Trust, The Primary Academies Trust and First Federation Trust.
At the other end of the table came the Education Fellowship Trust, United Learning, Gateway Academy Trust, The Collaborative Academies Trust, Ninestiles Academy Trust and the Woodland Academy Trust.
For writing progress, Outwood Grange Academies Trust was named as the best performer. It is based in Wakefield, and had three schools included in the figures.
It was followed by the Central Learning Partnership Trust, Hull Collaborative Academy Trust, Tudhoe Learning Trust, and the Harris Federation.
Academy trusts named the worst performers on this measure were Chulmleigh Academy Trust, the Blyth Quays Trust, Ninestiles Academy Trust, Schoolsworks Academy Trust and the White Horse Federation.
On the maths progress measure, the Central Learning Partnership Trust came top.
It was followed by Outwood Grange Academies Trust, St Barnabas Catholic Academy Trust, the Harris Federation and Phoenix Multi-Academy Trust.
Those named the worst performers were the Education Fellowship Trust, the Blyth Quays Trust, Gateway Academy Trust, the Woodland Academy Trust and Sharnbrook Academy Federation.