Ministry of Education deputy secretary Katrina Casey confirmed in a written statement the ministry had been advised of allegations regarding the professional conduct of Fairhall during the trip.
"The principal has returned home on the request of the Board of Trustees and will remain on leave while the allegations are investigated.
"New Zealand School Trustees Association is providing support to the Board of Trustees. We are also available to assist the kura as needed."
Ms Casey said the ministry would not comment further while the allegations were being investigated.
Mr Fairhall told the Rotorua Daily Post he would not comment as it was an issue between himself and his employer.
In a written statement tonight, Ms Ruwhiu said it was not appropriate to give details about the allegations but confirmed they had been made relating to Mr Fairhall's professional conduct.
She said the decision to bring the students home from Mexico was made after meeting with their parents and caregivers at a whanau hui where the board informed them a concern had been raised.
"They have been kept up to date. As the students have now been welcomed home and returned to their families, we will be sending a panui (notice) to the wider whanau."
She said returning home was in the interests of the whole group.
"We are committed to handling this sensitively for everyone and will be talking with individuals/whanau about what support, if any, they require.
"The Board takes all concerns seriously and will be investigating and reviewing all aspects of this situation."
This was the fourth time the school had embarked on a Mexico trip, which it does every three years. This year's trip cost each student $12,000, but thanks to three years' fundraising the end cost was brought down to $3500.
The trip, which sees students billeted with Mexican families to ensure immersion in the Spanish language, has become a part of the school's culture.