More than 400,000 children attend schools where pupils fall seriously behind in English, maths and science, league tables have shown.
Pupils at one in eight secondary schools in England make at least one term's progress less than expected between the ages of 11 and 14.
The league table results prompted calls for urgent action to tackle slipping standards in the first three years of secondary school.
The pattern emerged in tables ranking more than 3,000 schools on their national test results for 14-year-olds in maths, English and science "Sats" last year.
Figures showed pupils across England struggling with maths, as results fell nationally.
Tens of thousands of teenagers failed to keep up the progress they were making at primary school in the first years of secondary education.
Shadow children's secretary Michael Gove said: "It is deeply disappointing that yet another year has gone by with no improvement in literacy and maths results going backwards.
"Even more concerning is the fact that tens of thousands of pupils are making no progress at all between the ages of 11 and 14. We urgently need to deal with this problem with standards in the first three years of secondary school."
Schools Minister Jim Knight said: "The first three years in secondary school should provide pupils with a firm foundation to the rest of their academic life.(It) is not a time for coasting.
"I am impatient to see more progress made and see more pupils reach the levels expected for 14-year-olds."
