The strategy, which includes the literacy hour, will raise standards for all pupils, predicted Professor Michael Barber, head of the Government's standards and effectiveness unit.
But boys will remain just as far behind as they are now unless new measures - such as extra writing lessons - are introduced.
Addressing a central London audience, Professor Barber released figures showing that the gap between 11-year-old boys and girls has widened still further in the past year.
In particular, boys' performance in writing has dipped alarmingly.
Only 45 per cent of boys reached level 4, the expected standard in the latest tests, said Professor Barber - down by 3 percentage points. In contrast, 67 per cent of girls reached the target.
There is a similar gap in the reading figures, which show 79 per cent of girls at level 4 and 64 per cent of boys.
Overall, this year's English results showed a two percentage point increase over 1997, with 65 per cent of pupils achieving level 4 at age 11.
Ministers have promised that 80 per cent will reach this standard by 2002.
"The National Literacy Strategy definitely helps boys, but it helps girls just as much, so it doesn't narrow the gap," said Professor Barber, speaking in a lecture at the British Library, sponsored by Camden council in north London.
Research, he said, shows that boys have been helped by various approaches, which have also raised girls' achievement.
Other strategies would be needed to help boys. Professor Barber suggested that these could include additional writing sessions - on top of the literacy hour - for 10 and 11-year-olds, and special programmes to motivate infant boys.
* Primary schools need to spend Pounds 63 per pupil on books each year - with more than half of the cash being used to implement the literacy hour.
Research prepared by the Educational Publishers' Council, suggests that the literacy hour has made new financial demands on primary schools.
In the absence of official, national estimates of the cost of implementing the literacy strategy, recommended spending levels have been produced by the Book Trust, the educational charity.
The Government has put up some Pounds 20 million for books in schools and made additional grants.