The figures come from teachers' assessments of "non-core" subjects published this week, with breakdown by gender.
Just 58 per cent of pupils achieved the expected level 5 in a modern foreign language last year, and 15 per cent failed to get level 3 - which in other subjects would be expected at age 9. Figures show 20 per cent of boys failed to get level 3, and only 51 per cent have level 5.
It is also the subject which girls do least well in, with 66 per cent achieving level 5.
Dr Terry Lamb, senior lecturer in education at Sheffield University and chairman of the languages diploma development partnership, said: "The levels are supposed to be adjusted to take into account the fact the other subjects start in primary. This could be an indication of motivation.
"Children who are looking to drop languages in KS4 start to lose motivation in Year 9. We need to continue to focus on creating new courses in KS4 which pupils in KS3 will see as relevant and attractive."
The contrast with other subjects is stark. Tests in the core subjects show 73 per cent of pupils reach level 5 in science, 74 per cent in English and 76 per cent in maths.
Teacher assessments show that, apart from languages, achievement is similar across the board, with 74 per cent of pupils reaching level 5 in ICT, history and art, 75 per cent reach the expected level in geography, 76 per cent in design and technology, and 80 per cent in PE.
Concern over language learning has been growing since it became optional at key stage 3 in 2004, causing a huge drop in entries.
Last year, 216,718 pupils took French GCSE, compared to 331,089 in 2003. The changes to language learning at key stage 3 had a knock-on effect in key stage 4.
Nearly one third of schools have reduced lesson time for languages for 11- to 14-year-olds in the past five years, according to the 2007 Language Trends survey of 2,000 schools which is carried out by Cilt, the national training organisation for languages, and the Association of Langauge Learning.
National Curriculum Assessment at Key Stage 3 in England 2007 is at www.dfes.gov.ukstatistics.