The first national test results for five-year-olds show boys are behind girls on all measures.
More than 500,000 children have been assessed by their teachers against the foundation-stage profile - a list of 117 tickboxes.
Teachers have had to assess not only whether children can count to 10 and write their name, but whether they understand the difference between right and wrong or recognise the importance of staying healthy.
Teachers have criticised the results, which were published last week, as a waste of time and money. Some fear that publishing five-year-olds' scores in reading, writing and maths will put pressure on teachers to teach more formally.
The statistics show that more than half of children reach the expected level for five-year-olds in physical development, social skills and counting.
Children scored least well in literacy, where only 32 per cent reached the expected level in writing, and 36 per cent knew how to link sounds with letters in order to read more complex words.
Ruth Stott, headteacher of Elmbridge infants, Gloucester, said: "The paperwork is a nightmare. It is not what I want my teachers to put their energy into. I want them to work at teaching and developing a really creative curriculum, not ticking boxes."
Jenny Simpson, head of Lymington C of E infants, Hampshire, said: "Using observation as a way of assessing children is good. But these tests don't tell us more than we already know. Any good foundation stage should be focusing on children's social skills and physical development. On the continent children wouldn't even be in school."
But David Bartlett, co-ordinator for assessment at Birmingham local education authority, said: "It (the profile) covers the six areas of learning in the foundation stage because this was the strong preference of practitioners arising from national consultation carried out prior to the profile's development.
"It is designed to be used as an ongoing basis throughout the year, with judgments being made and recorded gradually."
The Government published the scores while warning that they incorporate inconsistent assessments and missing data.
Professor Peter Tymms, of Durham university, said: "If you ask teachers to rate children, they are inevitably influenced by gender. Girls are a little bit better at early vocabulary work and reading, but it is very slight and not educationally important."
"All this shows is that the arbitrary statements which were chosen to test development in personal, social and emotional development were easier than those for reading and writing. Those arbitrary decisions will now be used to blame teachers, quite wrongly."
But Dr Christine Skelton, of Newcastle university, felt it was not teachers who were biased, but the test itself. She said: "We know that girls gain language skills more easily than boys. This is not a problem, it is just the way children grow up.
"The foundation stage profile assessment scales are heavily reliant on language to communicate the child's knowledge and understanding. Even the maths section, a subject where boys have traditionally done better, requires them to articulate their thoughts for teachers."
The profile was made compulsory last summer. But the Qualifications and Curriculum Authority has already said it will be reviewed after a highly critical Office for Standards in Education report last month.
Officials had expected a teacher to take 35 minutes to complete one profile, but Ofsted found it took up to 90 minutes.
Unions have complained about the workload. The National Union of Teachers has said that it will consider balloting for a boycott.
David Hart, general secretary of the National Association of Head Teachers, said: "The foundation-stage profile is in dire need of a radical overhaul.
Early-years teachers have been grossly overloaded by a bureaucratic and time-consuming process which has produced results to which the Government has had to attach a health warning."
Mary Bousted, general secretary of the Association of Teachers and Lecturers, said: "This data is unreliable and unhelpful. The profile was implemented inconsistently because teachers received material, training and moderation at different times."
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