Teachers have declared they should not use their new powers to search pupils for weapons without consent.
School staff now have the legal authority to use force to strip off children’s jackets and jumpers and search trouser pockets for knives or guns.
But the Association of Teachers and Lecturers (ATL), representing 160,000 staff, advised its members not to frisk pupils without their agreement.
And parents’ groups expressed concern at Government guidelines which said the searches could be conducted by security guards who are not trained for work with children.
Ministers introduced the new legal powers for teachers to search pupils without consent in an attempt to cut violent crime and improve safety in schools.
But Mary Bousted, ATL general secretary, said teachers should call the police instead.
She said: “We do not consider it appropriate for our members to be involved in anything other than consensual searches of a pupil’s possessions and in examination of the contents of a pupil’s pockets should she or he voluntarily turn over the contents of their pockets to be searched.
“Should any other form of search be required of a non-consensual nature, ATL’s view is that its members should not undertake such searches.”
Education Secretary Alan Johnson said the new measures would send a strong warning to pupils thinking of carrying knives or other weapons into school.
Mr Johnson insisted the problem of weapons in schools was “very small”.