Revd Duncan Dormer has been speaking to Premier after the council sent a letter to thousands of parents which asks them to help their three and four-year-old children choose the gender "they most identify with".
The letter which is to be filled in before their children start primary school in September, also gives children the opportunity to leave the male and female gender boxes blank if they felt neither was applicable.
It said: "We recognise that not all children and young people identify with the gender they were assigned at birth or may identify as a gender other than male or female, however the current systems (set nationally) only record gender as male or female.
"Please support your child to choose the gender they most identify with.
"Or if they have another gender identity please leave this blank and discuss with your child's school."
The letter comes three months after the Council sent a survey to pupils at a secondary school in Hove with 25 gender options to choose from.
Revd Duncan Dormer is the Dean of St John's College, Cambridge, and specialises in gender issues.
He told Premier's News Hour: "Brighton and Hove's intentions are good and honourable, but this may just not be the right way of approaching it.
"They're looking at trying to create safe environments for young children, they're trying to prevent bullying, they're trying to recognise that people have different experiences.
"Part of the problem here lies with the notion that you read this form and then you sit down with your three-year-old very earnestly and talk about their gender identity, which is clearly a concept which they're not going to grasp.
"I think we should be very careful about what we're asking a three-year-old to do."
Brighton and Hove City Council's lead member for equalities, Councillor Emma Daniel, said: "Our pupil registration form asks for a range of information from parents and carers for children and young people of all ages who are entering a new school community.
"Parents and carers are asked to state their child's gender as male or female. For the vast majority of families this is very straightforward.
"By acknowledging the range of gender identities in our school communities we are helping ensure schools are safe spaces for everyone.'
