There has also been concern about the growing gender divide in achievement, starting in primary schools.
Under the synthetic phonics system, children are taught the sounds that make up words rather than guess at entire words from pictures and story context.
Rhona Johnston, a professor of psychology at Hull University, and Dr Joyce Watson of St Andrews University, studied the results from 300 children originally given training using synthetic phonics when they were five.
The progress of the group at primary schools in Clackmannanshire was compared with 237 children using the more usual analytic phonics approach.
Boys taught using synthetic phonics were able to read words significantly better than girls at the age of seven, with all pupils ahead of the standard for their age.
Boys were 20 months ahead while girls were 14 months more advanced than expected.
At the end of the study, boys' reading comprehension was as good as that of the girls, but their word reading and spelling was better.
"Teachers told us they had fewer disciplinary problems and less trouble in the playground because boys were succeeding and had higher self esteem."
Professor Johnston's work has been influential in persuading the Government to re-write its national literacy hour - returning to a system that dates back to Victorian times.
Synthetic phonics fell out of favour in the 1960s and 1970s in favour of progressive 'child-centred' learning that was championed for decades by educationalists in the Labour movement.
Boys do better than girls when taught under traditional reading methods
London Evening Standard