The gains are much less dramatic than those registered by the same pupils when they sat their key stage 2 tests five years ago, casting fresh doubts over one of Labour's biggest education success stories.
In 2000, the proportion of youngsters achieving the expected level four in English rose from 71 to 75 per cent; in maths from 69 to 72 per cent; and in science, from 78 to 85 per cent
Yet this week's results saw only marginal improvements in English and maths. In English, the proportion of papers graded C or better rose 1 point, from 59.9 to 60.9; in maths, results climbed 1.7 points, from 51.7 to 53.4 per cent.
The slump in languages also helped boost average grades as lower-achieving students deserted them. The A*-to-C rate for all subjects excluding languages rose only 1.6 percentage points.
The results are damaging for ministers because they suggest the apparent improvement in primary has failed to deliver gains for youngsters later on.
The 2000 test results marked the end of a period of rapid rises in the test figures, yet GCSE scores have improved only gently. In the 1999 tests, the proportion achieving level 4 rose in English from 64 to 71 per cent, and in maths, from 58 to 69 per cent. But GCSE results for the same youngsters last year saw only a 1.1 point improvement in the A*-to-C rate.
So, either the tests overstate primary improvements or pupils have not been able to maintain the progress they made in primaries.
This week, research for the Association of Teachers and Lecturers backed the first explanation. The Statistics Commission has also said test results overstated the rise in primary standards in primaries. The Government rejects this analysis.