Antibiotics have been administered to nearly 300 pupils at Mount Aspiring College in the past two days, in an effort to stop the spread of meningococcal disease.
Year 11, 12 and 13 pupils were given the antibiotic ciprofloxacin at the school on Wednesday and yesterday.
Public Health South staff will return to the school today to provide the medication to any pupils who had not yet received it and wanted to.
Some teenagers not enrolled at the school have also been offered the antibiotic, the Otago Daily Times understands.
The two pupils from the school diagnosed with the disease remain in Dunedin and Christchurch Hospitals, but their conditions have improved.
Tests from year 13 pupil Bella Berry (17) showed she had contracted the epidemic B strain of the disease, which was the seventh case in the Southern District Health Board area this year.
Technical reasons meant it was still unknown which strain had infected the other year 12 pupil.
Medical Officer of Health Dr Keith Reid had been at the school overseeing the antibiotic programme.
People believed to be at the greatest risk of carrying the meningococcal bacteria had been offered the antibiotics, Dr Reid said.
The risk to the wider community was low, but people should still remain vigilant for signs and symptoms of meningococcal disease, he said.
There is no information to suggest the pupils infected each other but the two cases may have originated from a similar source, he said.
No vaccine against meningococcal B is authorised for use in New Zealand.
