But at least three-quarters of seven-year-olds reached or exceeded these levels.
Welsh education minister Jonathan Evans, who announced the test results this week, said: "The performance of our seven-year-olds shows what can be done, and they have again set the standard of performance at which the 11 and 14-year-olds should aim.
"However, the performance of our 11 and 14-year-olds shows that a good deal of work still lies ahead. It is disappointing that 46 per cent of pupils are not attaining the levels expected of the vast majority."
Performance at seven was strongest in Welsh and science, according to the Welsh Office. In Welsh oracy, reading and writing, between 70 and 83 per cent of pupils reached level 2 or above. In English, 77 per cent reached the expected target in reading, and 78 per cent in writing. In mathematics, the figure was 82 per cent.
There are no science tests for seven-year-olds, but teacher assessment showed between 78 and 88 per cent of pupils reaching expected targets.
At 11, the best results were in science: 65 per cent reached level 4 or above in science; 57 per cent in English; 56 per cent in mathematics; and 54 per cent in Welsh.
But at 14, the best results were in Welsh: 69 per cent reached at least level 5 in Welsh; 56 per cent in English; 55 per cent in mathematics; and 54 per cent in science.