A study of 857 pupils in 28 state schools in England by researchers at York University found around one in seven had reading ages of two years or more below their actual age.
The study - co-authored by Dr Sue Stothard, Professor Maggie Snowling and Professor Charles Hulme - also found that 53 per cent of children with significant reading problems were on the special educational needs (SEN) register.
But a 15-year-old pupil who had a reading age of just eight years and nine months was not on the register.
The researchers added that, as some children may be on the SEN register for difficulties other than reading problems, the findings could be an underestimate.
Dr Stothard said: "It is a very important question for teachers and the Senco on how the SEN register is managed.
"Is it identifying all children with difficulties and making sure they get appropriate support."
However, Dr Stothard added that it was possible that some children would be identified as struggling with reading without being included on the register.
Brian Lightman, general secretary of the Association of School and College Leaders, said: "Secondary schools take literacy very, very seriously.
"They are absolutely committed to addressing this, because without addressing the basics children can't make progress.
"But whether they are put on the SEN register depends on what their literacy needs are."
Ofsted has previously criticised schools for being too quick to label children as having SEN in the past.
The Government is in the process of changing the system after concerns that over-identification of special educational needs can backfire because it risks teachers having lower expectations of those children.
- Read Sue Stothard's research white paper:
"The Rate and Identification of Reading Difficulties in Secondary School Pupils in England"