The results of new sample primary school science tests show that 19 per cent of pupils did not reach Level 4 - the standard expected of the age group.
This is an increase on the 12 per cent of pupils who failed to reach the standard in 2009, when all children were required to sit a national curriculum test in science.
For the first time this year, children were assessed by teachers for the subject, with 5 per cent of schools, some 27,210 pupils, also sitting a science test.
The Department for Education (DfE) which published today's results says they are not comparable with previous years.
But the drop in pupils reaching the expected level is likely to lead to suggestions that pupils had previously been drilled to pass the test.
In the past, English, maths and science national curriculum (Sats) test results have been used to create league tables for primary schools.
In the future, only English and maths will be used.
A note on today's statistics says: ''Comparisons with previous years are difficult as previous tests were taken under a policy of tests which fed the school accountability framework.
''These tests do not play any part in school accountability.''
It adds: ''The science sampling tests have been designed solely to give an estimate of attainment nationally and are not designed to be used as a tool to hold schools or local authorities accountable for pupil performance.''
This could mean that the tests were treated differently by primary schools this year, it was suggested.
Sion Humphreys, assistant secretary for the National Association of Head Teachers (NAHT), told the BBC website: ''It may well have been the case that given the fact that high stakes testing remained in English and maths that schools concentrated their efforts on these subjects.''
Today's results show:
:: Some 81 per cent of 11-year-olds reached Level 4 - the standard expected of the age group. In 2009, 88 per cent reached this level.
:: Girls did slightly better than boys (81 per cent of girls reached Level 4 compared to 80 per cent of boys).
:: Just over one in four pupils (28 per cent) reached Level 5 - one above that expected of the age group. In 2009, when every child sat a science test, 43 per cent of pupils reached Level 5.
Official figures published last week showed that an estimated 85% of pupils reached Level 4 in science according to teacher assessment.
Christine Blower, general secretary of the National Union of Teachers (NUT), said: ''There is a tell-tale clue within the Department of Education's press release which says it all. It admits that Key Stage 2 tests are about school accountability and not about assessing children's progress. The sample tests do just that. The introduction of National Curriculum Science in primary schools has been one of the great success stories of recent years.
''It is a success which is likely to be overshadowed in future by the obsessive focus on continuing to use English and Mathematics test results when judging schools.
''All in all, the sample tests point the way forward and I urge the Secretary of State to conduct his review of National Curriculum assessment with a view to putting the sampling system in place for both English and Mathematics.''
A DfE spokesman said: ''We are committed to raising standards in science at all levels, including Key Stage 2 by ensuring children are taught the fundamental scientific knowledge they need to progress - one of the main reasons we are not proceeding with the previous Government's planned primary curriculum is that it risked watering down traditional subjects.
''We also recognise that good quality science teaching is crucial if we are to get more children to engage and excel in their science education.''