It suggests schools log such incidents as well as more overtly homophobic remarks.
The booklet, Stand up for us: Challenging homophobia in schools, has been produced jointly by the Department for Education and Skills and the Department of Health and was sent to all schools in England this month.
The guidance tells teachers to challenge the use of "gay" as a generic insult, giving the example of a pupil who used the word to describe another's trainers.
Paul Patrick, a founder of the lesbian and gay teachers' group School's Out!, said it was important to make school staff think twice before referring to boys as girls. "Sexism and homophobia go hand-in-hand," he said.
The online resource suggests teachers put up flyers for Gay Pride marches and Mardi Gras festivals to show a positive stance on gay and lesbian issues.
It cites the case of a pupil excluded for accusing his teacher of being gay. "The boy observed the teacher on a bus kissing his girlfriend," the report said. The boy thought it "a blatant display of romantic sentimentality" and that "as such a public act of affection towards a female was so unmanly, the teacher had to be gay".
The report said: "Young people inhabit a society where they learn that sexual reputation is very important to social status and sexual difference can mean a threat to that status."
Stand Up for Us is available at www.dfes.gov.uk