Figures from exam board AQA show that most teenagers failed to achieve a level 3 pass - the standard expected of candidates who achieve good GCSEs.
At one school in York, just four out out of 35 candidates passed information technology, in the "communication" (English) exam, three-quarters failed and, in use of number, just two out of 13 made the grade.
The figures will fuel school and college fears over the new qualifications, introduced in September as part of the Government's post-16 reforms.
A recent survey by the Secondary Heads Association criticised the rushed introduction of key skils and said students were not taking the qualifications seriously because universities did not require it.
About 10 per cent of the million sixth-formers taking key skills sat the exam in January. More than a quarter took the AQA papers.
Students take an exam and complete a portfolio in each of the three subjects. To get the qualifications, which count for 30 university entry points on the new UCAS tariff, students must pass both the coursework and the test.
It is unclear if other exam boards have experienced similar failure rates. Exam watchdog, the Qualifications and Curriculum Authority, refused to reveal the national picture. A spokesman said: We do not publish results until the whole assessment is completed."