The guidance also says schools should have a policy for teachers asked about topics restricted to older children.
This may include asking a pupil to speak to their parent or signposting support services where needed.
Announcing the guidance, Mr Sunak said: “Parents rightly trust that when they send their children to school, they are kept safe and will not be exposed to disturbing content that is inappropriate for their age.
“That’s why I was horrified to hear reports of this happening in our classrooms last year”.
Ms Keegan said the new guidance had been motivated by a request from teachers “to provide more clarity” on age-appropriate sex education, but she had also seen reports of “campaign groups’ or lobby groups’ materials” being used in classrooms.
She said she had received evidence of lesson slides including “things like choosing lots of different genders and identities and saying which ones of these are gender identities – the spectrum. The sort of, ‘it can be a spectrum, it’s fluid, you can have different genders on different days’ or ‘there’s 72 of them’. That kind of thing”.
The education secretary admitted to BBC Radio 4’s Today programme that she did not know how widespread the issue was as “it’s not something that we’ve gone and done a particular survey of”, but said she did not think it was common.
Shadow education minister Catherine McKinnell said she was pleased the draft guidance had at last been published but there was “deep concern about the lack of consultation with school leaders in developing the guidance so far”.
“Teaching children about the facts of the world in which they grow up must include an understanding that there are people who are transgender, that people can go through a process of change of their gender and that the law provides for that,” she added.
Other elements of the guidance include advice for teachers about how to address misogynistic online influencers, the benefits of rationing time online and information on miscarriage and pregnancy loss.
Speaking to BBC News on Wednesday, some parents welcomed the idea of restrictions on sex education.
But others pointed out a danger because if children could not receive information about certain topics from their teachers, they were more likely to take in potentially harmful content looking for the answers online.
Lucy Emmerson, chief executive of the Sex Education Forum, said: “If topics were to be restricted it will leave children even more dependent on getting answers about topics from pornography, coercive control and STIs [sexually transmitted infections] from online sources.”
Ms Keegan said children under the age of nine could still be taught about conception as it could be discussed “in a very factual, scientific way”.
The draft guidance is now open to a nine-week consultation, external.
Once finalised, it will be statutory and schools will be expected to follow it.