The city's ranking has sunk to fourth from bottom in a table of 150 local authorities across the country and 12 of its primaries have been named among the worst 200 performing schools in the country.
More than one in 10 of England's worst achieving primary schools are in Yorkshire.
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Sheffield's worst performing school, Bankwood Primary, achieved the fifth lowest scores in the country with less than a quarter of its pupils reaching the expected level in English and maths key stage two curriculum tests.
And five more of the city's primaries were named among England's 100 worst performing schools.
But Sheffield Council defended the record of its primary schools, although it accepted a small number had low attainment.
The league tables published today by the Department for Children, Schools and Families show how every school in the country performed in key stage two standard assessment tests in English, maths and science sat by 11-year-olds this year.
Record numbers of primary schools scored full marks in the tests this year with 250 primaries, including 18 from Yorkshire, succeeding in making sure every 11-year-old reached the standards expected of them, known as level four, across the three subject areas.
However, the figures also confirmed that three out of 10 pupils across the country failed to master the basics of both English and maths.
Every education authority in Yorkshire saw improvements in their results compared with last year but Sheffield failed to keep pace with other authorities and slid from 10th bottom to fourth bottom in the country ahead of only Hackney, Bristol and Leicester.
In contrast Bradford, which last year finished second bottom of a national league table, saw its pupils achieve the fourth most improved results in the country.
A major investigation into standards in primary schools was launched last year after results saw Bradford ranked 149th out of 150 local authorities. This year's results saw the city rise to 136th in the country.
Coun Colin Gill, Bradford Council's executive member for services for children and young people, said: "These results are fantastic and we should all join in congratulating teachers, governors, parents and pupils on their achievements.
"Improvement takes time and we are seeing the culmination of several years' work."
Defending Sheffield's record, the council's executive director of children and young people's service, Jonathan Crossley-Holland, said: "Although we have not moved up the league tables our results have improved faster than the national average, almost twice as fast for English and science on both the level four and level five measures – the gap between Sheffield's attainment and the national average is beginning to close."
He said the authority had provided focused support at 25 primary schools which would result in more rapid progress in future.
Elsewhere, Leeds climbed 11 places in the league tables overtaking Kirklees and Wakefield to become the region's fifth best performing authority while Barnsley and Rotherham finished in the bottom 20 nationally.
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