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The gap between SEN pupils and their peers has risen from 48 percentage points in 2016 to 52 this year.
The figures were revealed in school league tables published by the Department for Education (DfE), showing the results of approximately 16,000 primaries.
Head teachers say that special-needs education funding is in crisis and partly to blame for the gap widening.
The government statistics show 18% of children with SEN reached the expected level in reading, writing and mathematics, compared with 70% of their peers without special needs.
Although SEN pupils' results edged upwards on last year, when 14% made the grade, their non-SEN peers boosted their results more dramatically from 62% to 70%.
Teachers have been warning that pupils with special needs, such as mild autism or dyslexia, would struggle in the tougher tests that were introduced last year.
A National Association of Head Teachers' spokesman said it was "one of those situations where money is the solution and schools need the government's help".
The tables also showed disadvantaged pupils still perform far worse than all other pupils in England, with around half passing the tests, compared to nearly two-thirds of non-disadvantaged.
This represents a problem for the Government as the gap between the two groups of pupils is now as wide as it was in 2012 at around 20 percentage points.