The group had been due to return to New Zealand on Saturday.
The Johnstons, who were in their late 50s, had 10 children and were a founding family of Bethlehem College.
Bethlehem College pastor Craig Vernall told 3 News it was a "real blow'' to the school.
"We've got to handle the situation with kid gloves, we've got some really, really hurting people,'' he said.
"There were a number of Kenyans, two or three, who were also killed in the accident with the three from the school.'' A Rotorua teacher was among those injured. Gemma Tong, a teacher at Rotorua's Chapman College, suffered a broken arm.
Rotorua's Chapman College is modelled on Bethlehem College which was founded by Graham Preston in 1988.
Mr Preston had known the Johnstons since they enrolled two or three of their children when Bethlehem College first started.
Mr Preston is now the principal of Chapman College and said Miss Tong had broken her arm in a few places and was still in hospital. Another teacher was understood to have broken bones while team leader Philip Russell suffered concussion.
Mr Preston's granddaughter, Amy Bell, 17, was also on the bus. He said he wasn't sure whether she had been discharged from hospital but had heard she was "resting comfortably''.
Mr Preston said Miss Tong had commuted to Chapman College with him from Tauranga and she had talked about how excited she was about the trip, raising $6000 to go on it.
The 25-year-old had been looking forward to working alongside other teachers in Kenya and helping them.
"Her real passion is teaching and the art of teaching.''
Mr Preston said he was at a loss to say why it happened but said Christians were not immune to difficulties.
"There is no answer. Bad things happen to good people. Bad things do happen. It's how we deal with it, that's where the grace is.''
Chapman College is situated at Living Well Church and one of the pastors, Gary Ellis, said he was still trying to find out what had happened. Mr Ellis said Miss Tong, who was formerly a teacher at Bethlehem College, loved Chapman College and the concept of it.
A Ministry of Foreign Affairs and Trade spokesperson said the ministry was aware of "a motor vehicle accident in Kenya involving students from Bethlehem College in Tauranga".
"The New Zealand High Commission in Pretoria is providing consular assistance and support. We are unable to release further details at this time."
As news of the tragedy broke this afternoon Bethlehem College staff and families of the 12 students in Africa closed ranks and declined to give any information about what had happened.
Murang'a South traffic boss Loise Gatimu told a local reporter for The Star that the road where the crash happened was notorious for bad driving.
She said most accidents in the region had been caused by careless drivers.
"We are losing too many innocent lives on this road that has turned into a nightmare to residents due to careless driving. The rising carnage can only be checked if drivers observe traffic rules.
"It is sad that we have lost one life," Gatimu said.
In November, some of the students spoke about the upcoming trip - which they were looking forward to.
It was the third time that the college has sent volunteers to the Ark Quest Education Centre, where they were set to spend their time painting, building, teaching, visiting and "generally helping out wherever they are needed".
Before the trip associate principal Phillip Russell told the Bay of Plenty Times that he believed the journey was life-changing for the students involved.
"When we visit Kenya, the students get as much as they give. They come home with a whole new perspective about what's important in life and most get really excited about making a difference here in their own community"he said.
Each student had to raise $5000 to fund their trip, and they had been fundraising for months in the lead up to it.
The college website still had information about the trip last night.
"The team will be based in Ma'hanga Village in the Vihiga District of the Western Province. The team will be involved in improving the school's facilities (painting, making shelves and creating resources). There will be a strong focus on building relationship with the community and being part of village life. Students will also be involved in daily devotions with a clear intention to strengthen their character."
The group were being hosted by the village in a local house and were eating traditional Kenyan food during their stay.
Dr Johnston was an anaesthetist for the Bay of Plenty District Health Board.
In a statement the DHB said today was the anniversary of the beginning of his career with the board where he had been "a dedicated member of staff for the last 26 years at both Tauranga and Whakatane sites''.
"Five years ago, and seeing a need for providing stability at Whakatane, Brian volunteered to take the anaesthetist's position and travelled from his home in Tauranga weekly to be an active and respected member of the Whakatane Hospital community. Brian was a dedicated Christian who was described by his colleagues as 'the nicest person you would ever meet' and someone who `would only ever give, never take.'
Dr and Mrs Johnston were described as "being woven into the fabric of the Bay of Plenty'' and would be sorely missed.
They left behind a large family and a number of grandchildren.
"Our thoughts are also with our other members of staff who have children on the Bethlehem College mission in Kenya.''
