David Bell, who heads Ofsted, said that one in four pupils fell short because too many teachers were unclear about how best to teach the basics of reading and writing.

They were unsure how to work with small groups of pupils on reading, spelling and phonics — the way letters are spoken and linked together to form words.

Mr Bell also said that the weak leadership and management of one in ten head teachers exacerbated the problem. He ordered a review of the way that literacy is taught in primary schools.

The Government has spent millions of pounds on its twin literacy and numeracy strategies, which were the cornerstone of its manifesto in the 1997 election campaign. It promised to increase the number of 11-year-olds reaching level four in Key Stage Two tests to 80 per cent in literacy and 75 per cent in numeracy by last September.

The failure to hit the targets — they were 75 per cent and 73 per cent respectively — was a factor in the resignation of Estelle Morris last month.

Last year she claimed that she had never promised to resign if the targets were not met. However, the Conservatives checked parliamentary records and found that she had made the pledge as School Standards Minister in 1999.

The report also noted the persistent gap in performance between the sexes: 83 per cent of girls reached the required standard in reading, compared with 77 per cent of boys. Only 52 per cent of males achieved it in writing, against 68 per cent of girls.

Earlier this week, Mr Bell said that he was relaxed about the “gender gap” because girls needed an academic headstart to make up for discrimination that they would suffer in the workplace.

He conceded that the strategies had brought about substantial overall improvements in academic performance, but a fall in reading results for two successive years needed to be addressed. He has ordered his inspectors to conduct a national survey of the way reading is being taught.

“The strategies continue to have a positive impact,” he said. “But I am concerned that there is still a stubborn core of weak leadership and management where head teachers do not do enough to make a difference to the standards in their schools.”

In a separate report on numeracy strategy, Mr Bell said that although pupils were not as good at mental arithmetic as they should be, the strategy was broadly successful.

David Hart, the general secretary of the National Association of Head Teachers, said that the finding that heads were weak in 10 per cent of schools was in line with expectations. “I think a 90 per cent approval rate would be something that most professions would be pretty pleased with,” he said.

David Miliband, the School Standards Minister, said: “Primary standards have made huge gains since 1998 and this year’s results are the best ever. However, we are not taking our eye off the ball. Primary standards are the cornerstone of success in education and we will continue to focus our efforts on raising standards.”

Damian Green, the Shadow Education Secretary, said: “The current literacy strategy will not solve one of the biggest crises in our schools — that a quarter of 11-year-olds leave primary school unable to read or write properly.”

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