In a letter to staff and parents, board of trustees chairman Trevor Thomson said Mr O'Brien would be off work from next week, and it was hoped he would only be away for about four weeks.
''Although it could extend to the end of the term,'' Mr Thomson said.
''The outlook for Mr O'Brien is very positive and I know we will all support him through our good wishes and prayers.''
He said deputy principal Steve Read would be acting principal and Trish James would be acting deputy principal.
Mr O'Brien reassured the school community yesterday he was fine.
''It's not a life-threatening matter, but it does need to be sorted out.
''I could have possibly worked through it, but the treatment will require me to be in and out of the office.
''To continue working would cause more problems logistically and there would be uncertainty about whether I'm here or not here on any given day.''
It was important to have one leader who was constantly running the school, he said.
