Senior pupils at Mount Aspiring College received the antibiotic ciprofloxacin in pill form, yesterday.
Another antibiotic, rifampicin, was given to pupils unable to take ciprofloxacin.
Both would clear the meningococcal bacteria from the throats and noses of carriers.
Pupils were offered the antibiotic after two pupils were diagnosed with meningococcal disease within a week of each other.
Public Health South medical staff would remain at the school today, to ensure all senior pupils could be given the treatment.
Principal Wayne Bosley said he was very pleased by the way pupils and staff had co-operated with the medical team.
''It's obviously been a pretty testing time for the entire school but the community is very close and has come together to work through this,'' he said.
Acting director of public health Dr Stewart Jessamine said so far this year 12 cases of meningococcal B, seven of which were the epidemic strain, had been notified in the Southern District Health Board area.
The ministry was working with Pharmac to source a rapid supply of the meningococcal B vaccine to be used if the number of cases in the southern area increased, Dr Jessamine said.
Between 2004 and 2006 the vaccine was used in the meningococcal B immunisation programme offered to anyone under the age of 20.
It was no longer available in New Zealand.
One of the pupils, Bella Berry, (17), was infected with the epidemic B strain.
The strain from the second year 12 pupil was still being investigated.
Bella's condition had improved and she was expected to make a full recovery.
The other pupil had been moved from the intensive care unit at Christchurch Hospital and was in a comfortable condition.
Mount Aspiring is not the first school in Otago to undertake a large-scale meningococcal disease medication programme.
In 2002, all pupils at South Otago High School were offered the meningococcal C vaccine, after four pupils from the school and two from neighbouring Rosebank Primary School contracted meningococcal meningitis.
Wayne Dixon, who was principal of the high school at the time, said it had been a testing time for both schools and the South Otago community.
He was pleased to see steps taken to manage the outbreak at Mount Aspiring.
