Fewer than six in ten 14-year-olds reached an acceptable standard for their age in the three Rs this year, according to teacher assessment results published last week.
The performance of teenagers in reading, writing and maths was rated by teachers and then broken down by Assembly government officials for the first time.
The figures reveal almost 15,160 of the 2008 key stage 3 cohort of 36,266 - or 41.8 per cent - did not score the expected level 5 or higher in literacy and numeracy.
The results will validate growing concerns over the academic performance of Wales's teenagers compared to the other home nations as well as globally.
Calls for an investigation into the age group's poor performance have been growing since the low ranking of Wales's 15-year-olds in reading and maths in last year's Pisa tests (the programme for international student assessment).
But an Assembly government spokesperson said the 14-year-olds' results were not "particularly low."
"They are (the cohort) where we would expect them to be given performances in the different assessment components," she said.
Last week, an official Assembly government press release praised an improvement in overall performances across the board and the swift and efficient collation of the data by a new electronic system.
Dr Philip Dixon, director of the Association of Teachers and Lecturers Cymru, said that despite the "worrying" tail off at KS3, results showed encouraging signs of progress in a Sats-free Wales. He said teacher assessment was now giving a truer picture of children's achievements than the discredited testing system in England.
"The value Wales now places on professional judgment is only heightened by the contrast with the costly and discredited Sats fiasco over the border," he said. "The progress made in Wales is also not producing the emotional turmoil in children's lives caused by those now discredited tests. What we have here is a snapshot of the reality of where our children are, not a picture distorted by obsessive teaching to the test which characterises the Sats regime."
The percentage of 14-year-olds in the most deprived local authority of Blaenau Gwent who failed to reach the expected level for the three Rs was 45.7 per cent this week - more than 20 per cent less than the highest scoring, Monmouthshire.
Overall, 59.6 per cent of 14-year-olds achieved the expected level or higher in the core subjects of English, Welsh, maths and science. But those reaching an acceptable age level in reading and writing and maths are lower, at 58.2 per cent; in England, the percentage would be considerably higher at 74 per cent.
At KS1, there was a tiny percentage drop in standards in the three Rs this year: 74.6 per cent reached the expected level 2 or above. But the cohort performed slightly better than last year in core subjects overall.
At KS2, 11-year-olds reaching the accepted standard were up by more than one percentage point. The reading, writing and maths average was also up to 69.3 per cent, making the age group the highest performers.
Professor David Egan, education adviser to Wales's former education minister Jane Davidson and director of the Institute of applied education research at UWIC, Cardiff, said more research was still needed to attack apparent downturn from KS2 to KS3.