The victim lay on the field in agony until he was eventually stretchered off the field and taken to hospital. He is now recovering from his injuries.
"Apparently they weren't wearing anything apart from the helmets," a source said.
Posts on social media refer to the boy's wound as a "very deep cut", possibly caused by the motorbike pedal hitting his leg.
"Doctors said it's actually down to the bone."
Another source told the Herald the annual streaking prank had been occurring since at least 2009.
A student told the Herald teachers had been aware of the prank for the past three years and stopped it.
"However this year they used motorbikes."
Other reports say the girls were wearing underwear, shoes and helmets and going a "decent speed".
Police told the Herald the victim suffered moderate injuries and was taken to hospital.
Waikato Police Senior Sergeant Ray Malcolmson said the prank happened just after midday and police rushed to the school after receiving a call from ambulance staff.
It is understood the boy's family are speaking to police today.
"There was a collision with a bike and a student on the school grounds. The student has suffered moderate injuries and has gone to hospital," police said.
Waikato Diocesan principal Mary Curran confirmed six senior students were involved in the "unfortunate" prank.
Curran said school authorities were helping police.
"This is unacceptable behaviour, which we are taking very seriously," she said.
"Due school process will be followed."
Curran said she wished the injured student a speedy recovery.
Hamilton Boys' High School principal Susan Hassall told the Herald: "I am unable to make any comment at this stage, as I have been away from the school at a meeting through the afternoon and early evening."
She had earlier confirmed "uninvited" students from another school entered the grounds.