National Challenge affects secondaries where fewer than 30% of pupils get five good GCSEs including English and maths.
The "floor target" for primaries will involve the percentage of 11 year olds achieving the level expected for their age in both English and maths "Sats".
A head teachers' leader warned thousands of schools could fall below.
A spokesman for England's Department for Children, Schools and Families (DCSF) said: "We have always made it a key priority to improve all schools.
"We believe that it's right to insist on certain minimum standards in the system, because that's what parents want.
"Our role has been, and will continue to be, one of stretch and support for schools."
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