Teachers held an emergency assembly to explain the matter to confused pupils and tell them they should now treat the child as a girl.
"We are committed to ensuring the best for our child. We are working with other agencies to ensure our child's welfare is protected," his mother told The Sun.
However, parents of other wards were displeased and said that the head teacher should have warned them before the school's announcement to their children.
"They behaved appallingly by throwing this hand grenade into the room and then leaving the inevitable questions about it for unprepared parents,' one mother said.
"Maybe we could have explained sexual politics and encouraged our kids to be more sensitive if we''d had a chance to be involved."
The boy, who always wanted to be a girl became the world's youngest sex change patient.
He is now preparing for hormone treatment and ultimately surgery, which the law would permit once he reaches puberty.