Seven academies were named among the worst schools in the country in league tables published this week.
Of the 13 privately-sponsored academies that have been open long enough to be included, seven appeared in a table of the bottom 200 state schools for key stage 3 results.
However, ministers said it was still too early to judge academies'
performance, insisting that results in the tests for 14-year-olds showed the schools were improving fast from a low base.
On average, the improvement in academies' KS3 results since last year - in English, maths and science - is three times that of other schools.
Lord Adonis, schools minister, said: "You can't criticise academies for not yet being at the top of the performance table when they started the game behind on penalties thanks to poor standards at the failing schools they replaced.
"But they are getting there, as results show, they are improving rapidly and will be among the very best schools in the future. Success for 14-year-olds in these tests is a key indicator they will do well when they take GCSEs."
Nationally, KS3 results continued to rise across England.
Compared with 1997, in 2005, 102,000 more 14-year-olds reached at least the target level in English, 84,000 more reached it in in mathematics and 60,000 more did in science. The top performer in the country was Reading grammar, while Whitstable community college in Kent was named most improved school.
But there were notable failures among academies. At Manchester academy, sponsored by the United Learning Trust, a Christian charity, the average points score in the 2005 tests was 26.8, compared to the average in all English state schools of 34.5.
Manchester's results were worse in the latest tables, based on the 2005 tests, although Ofsted recently graded it "satisfactory" overall.
Other academies with particularly poor results included the Capital City, in north London, Unity City in Middlesbrough - which has been failed by Ofsted - and City academy, Bristol. The results for the last two schools improved on the previous year, but Unity's remained the same.
However, the number of academies among the bottom 200 schools fell from nine in last year's table to seven this year.
Steve Sinnott, general secretary of the National Union of Teachers, said:
"It must be a great disappointment to the parents who believed the Government's publicity that just calling a school an academy and bringing in a commercial sponsor would result in substantial improvement."