Professor Jim Conroy, from the school of education at Glasgow University, said the widespread use of synthetic phonics at the expense of other methods is damaging reading in the long term.
Synthetic phonics, where children learn the sounds of groups of letters rather than whole words, has been adopted in many schools across Scotland in recent years. A seven-year study by researchers at St Andrews University found children taught under the method in Clackmannanshire were more than three years ahead of their chronological reading age by the time they left primary school.
After the report's publication in 2008, Peter Peacock, the former Labour education minister, wrote to all primary headteachers highlighting the positive results.
However, Mr Conroy believes widespread adoption of the technique can be harmful because pupils grow up knowing how to pronounce words without necessarily knowing what they mean.
He argues the technique is labour-intensive and undermines the natural pleasure pupils get from reading stories.
In December, a report found secondary pupils in Scotland had made little progress in reading compared to other countries.
Mr Conroy said: "If synthetic phonics was the silver bullet that has been suggested we would have seen an increase in reading skills in the latest international comparisons, but that has not happened.
"A lot of the evidence suggests synthetic phonics can have an initial impact, but that there is no long-term gain. What we need is a blend of techniques, but also a return to reading stories with children that they enjoy so we are fostering a lifelong engagement with the written word."
Mr Conroy believes the "fad" was promoted by small councils concerned about future viability that wanted to be seen as being at the cutting edge of education.
With synthetic phonics, pupils are encouraged to blend letter sounds from the beginning of their education so they understand how words are put together.
Under more traditional analytic phonics, children are taught whole words and only learn the individual sounds of key letters, such as the initial letter. Analytic phonics is slower because children are taught sounds over a longer period and can struggle to blend them into more complicated words.
The technique produced startling results in Clackmannanshire and West Dunbartonshire, where a decade-long strategy let to the council announcing it had "eradicated" illiteracy.
The West Dunbartonshire strategy was aimed at young children in the poorest areas, and delivered by specialists based at Dalreoch primary in Dumbarton. In 1997, 5% of children in the first year of primary school in the area had "very high" scores on word reading. A decade later the figure was 45%.