Phillipa Smith, an agnostic, said the child's right to an education free of religion had been violated by Siskin infants, in Gosport, Hampshire.
She says that when she complained to the non-church school, five-year-old Willow was made to stand by a classroom door as other children sang.
"When I enrolled her I was told the only religion she would be subjected to was a few songs," she said. "But thanking the Lord for the food they are about to eat and asking God to guide them home safely clearly goes beyond that. I don't think any child should be force-fed religion."
Rose Smith, headteacher, said the school was merely abiding by the law requiring pupils to take part in daily acts of collective worship. But she admitted that saying grace could be considered by some parents to go too far. "Teachers have not meant to cause offence," she said. "But we have sought advice and we are now going to review the policies of the school."
Last year David Bell, the chief inspector, called for the requirement for daily collective worship to be dropped, saying three-quarters of secondaries no longer complied with the 60-year-old legislation. But critics say the row at Siskin infants reflects a growing trend among community schools to promote religion amid government support for the expansion of faith-based education.
Marilyn Mason, education officer for the British Humanist Association, said she was also aware of a school using creation stories in the literacy hour and a child from an openly atheist household being criticised by an evangelical Christian classroom assistant. "The current political climate, in which the Government supports faith-based schools, seems to have made some schools less inhibited about being overtly and evangelically religious," she said.