The report has been published to review the first year of the literacy strategy, the focus of which is the daily literacy hour.
School inspectors say that while the government's national literacy strategy has helped boost literacy standards, the quality of pupils' writing is still lagging behind their achievements in reading.
The report by the Office for Standards in Education (Ofsted) says poor standards in writing are particularly noticeable among boys.
It says more attention should be given to training teachers to teach writing effectively.
And it calls for a review of the balance between the time given in schools to the teaching of reading and writing.
The government has already announced plans to introduce new spelling tests to help raise literacy standards.
The report has been published to review the first year of the literacy strategy, the focus of which is the daily literacy hour.
Inspectors found that the quality of teaching of the literacy hour had improved throughout the year, but there were continuing problems with the teaching of phonics, which was weak in many schools, particularly for eight to 10-year-olds.
Their report also points out a considerable gap in achievements between girls and boys.
In national curriculum tests, only 46% of 11-year-old boys achieve the national expectation in writing, compared with 61% of girls.
Graduates' grammar
The Chief Inspector of Schools in England, Chris Woodhead, said there was "no doubt" that the national literacy strategy had improved the quality of teaching of literacy.
But he said: "This report reveals a number of worrying issues. Among these, the continuing weakness in phonics teaching in Years 3 and 4, the comparative lack of progress in writing, and the poorer performance of boys at all levels are the most serious."
He also said he was "deeply disappointed by the variable performance of LEAs in implementing the strategy.
"Too many failed to set effective literacy targets, while others were slow to give the strategy sufficient priority at the beginning of the year."
Speaking on BBC Radio 4's Today programme on Tuesday, before the publication of the report, Mr Woodhead said many university graduates could no longer write a grammatical sentence.
"That is why we need the national literacy strategy," he said. "We have got too many people who are achieving degree level who haven't mastered the rules of basic literacy.
"I think the only way forward is to go back to the beginning, as the government is, and make sure the foundations are laid properly in primary schools in a way that they were not for a good number of years."
In response to the Ofsted report, School Standards Minister Estelle Morris said every teacher of pupils aged 10 and 11 was being trained in the teaching of writing this term and next.
Booster classes for Year 6 children, being held since the autumn, had a new focus on writing, and a national writing competition for primary schools would be launched in the new year to encourage all children to develop their writing skills.
The government would also publish guidance next term to help schools' tackle boys' underachievement in literacy.
She said: "Ofsted's report makes it clear that the national literacy strategy is already making an extremely positive impact on teaching and learning."
The government had anticipated that progress in writing would not match reading, but there had been a small improvement in writing test results this year.
"We are aware that some LEAs have done much better than others in implementing the strategy, but they are all monitored regularly by our network of regional directors, and action is taken where weaknesses are identified."