The union claims parts of the new Employment Equality (Sexual Orientation) Regulations 2003 have no legal basis in European law.
And it believes that the regulations breach human rights because they give faith schools too much scope to discriminate against gays and lesbians on the basis of their sexual orientation.
"Committed teachers in faith schools may become vulnerable to misinformed or over-zealous application of the provisions," said an NUT spokeswoman.
"Some organisations that run independent schools have said they will use this law to ensure no lesbians or gays are employed," she added.
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