In the first incident revealed yesterday, a student thought to have been aged 14 or 15 got down to her underwear and fishnet stockings, while holding a sign saying "toot for a strip".
A male coach was accompanying her and other students, while the school's van - with the logo emblazoned on the side - was parked nearby on Fenton St in central Rotorua.
In the second incident, students visited a nearby Pak'n Save, with one girl wearing only a swimsuit.
The communications manager for the $20,000-a-year school told the Herald: "Our understanding of this situation was that the girl was carrying out a prank put to her by her teammates, who were around the supermarket, wearing mufti."
The principal Lynda Reid denied rumours the student was topless, and said another allegation, involving a student being tied to a pole, was untrue.
Rotorua Bike Barn employee Ruthy Arrowsmith, who witnessed the stripping incident, said she spoke to a man and two women who appeared to be supervising the students.
"They told me it was like an initiation. They all seemed to be bragging about it, one lady even told me that the girls had run through a supermarket earlier, carrying a towel, screaming for shampoo, naked," she said.
"I thought, 'are you for real?' These are girls that are from an esteemed college, and are the young leaders of tomorrow."
Ms Reid said the school was taking the stripping incident "very seriously" and would conduct a "thorough investigation". "The coach ... was not an employee of our school but a professional working on a paid external contract.
"The coach has been stood down while the investigation is conducted. The team was sent home from Rotorua when the school was alerted to the behaviour.
"As a school we are viewing this incident very seriously and I apologise to the people who were upset by the student's behaviour however ... this was the behaviour of a young student who did not consider the consequences of her actions."
The tournament organisers, New Zealand Secondary Schools Football, will also investigate.
"We wouldn't condone any behaviour like that," said Leigh Perry, national administrator.
