The Christian Institute said it was "totally misleading" to let children choose options including "gender fluid", "genderqueer" and "non-binary".
Youngsters aged from 13 to 18 were asked to select from 25 choices which also included traditional options of "girl" and "boy".
The national survey was linked from the website of the Children's Commissioner for England, Anne Longfield, and was forwarded to some schools by local councils.
The Christian Institute's spokesman Simon Calvert said: "We must not intrude on childhood by deliberately confusing schoolchildren about what makes a boy a boy or a girl a girl just to satisfy adult political agendas.
"We must protect children from being made to feel that passing phases of confused feeling about themselves, which many go through, must be turned into life-changing moral and political decisions."
The survey has now been withdrawn and the Children's Commissioner for England claims it was a ""clerical error" and only a draft.
A spokesperson said the survey will be redrafted with only two gender options.
A Brighton and Hove City Council spokesman, which forwarded the national survey to all its secondary schools at the request of Ms Longfield's office, said it was aimed at exploring young people's experiences of gender.
The spokesman said: "We want all our young people to feel comfortable with who they are, to understand that the notion of gender can go beyond the traditional idea of simply being either male and female, and to recognise that people can use a range of terms to describe their gender identity."