Dr Emma Wood spoke to the students in September as part of the school's Christian education curriculum. Wood runs the anti-abortion "Pro-Love Logic" organisation and gives presentations to help students understand the relationship between "widespread abortion and the individualistic sexual culture the West has embraced".
Principal Scott Marsh sent a letter to parents of year 11 students on Friday after commissioning an internal review.
"I am ultimately responsible for activities involving our students," Marsh wrote in the letter seen by The Age.
He said the review found procedural failings in how the presentation was arranged and managed.
"The presentation should have been classified and managed as an incursion because it involved an external speaker addressing boys outside the normal class timetable," Marsh wrote.
The principal described the episode as a clear failure in processes.
"We are sorry for the distress this caused some boys and families," he said.