Secondary schools in Lambeth and Merton failed to make the grade in the national key stage 3 exams.
Lambeth's borough average of 33 and Merton's of 33.9 fell below the national average of 34.9 in the exams sat by 14 year olds last May.
Croydon and Wandsworth narrowly missed the national average, scoring 34.4 and 34.2 respectively.
The figures, released today by the Department for Children, Schools and Families (DCSF), show Hounslow met the national average of 34.9 in the English, maths and science tests, while Richmond exceeded the target with 35.5.
Sutton and Kingston were among the best performing LEAs, with average point scores of 38.3 and 38.
Students at Sutton Grammar School for Boys and Tiffin School in Kingston who sat the exams all passed with flying colours.
And at Tiffin School for Girls there was a 100 per cent pass rate in science and 99 per cent of pupils made the level 5 grade in English and maths.
Surrey LEA had an average point score of 36.1, above the national standard.
Schools Minister Jim Knight said some schools had made excellent progress but pupils in some areas were still falling below national standards.
"It's crucial that other schools learn from their example - the first three years in secondary school should provide pupils with a firm foundation to the rest of their academic life and is not a time for coasting.
"The key stage 3 results give a good indication of how pupils will achieve at GCSE and I am impatient to see more progress made and see more pupils reach the levels expected for 14 year olds."
To view the key stage 3 results for schools in your area click here and search for your LEA under secondary schools.
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