Principal Jill Farquharson said the school immediately followed procedures in place to manage situations "such as this". The police were involved and they had worked with the school, she said.
"Good news is the student was located and is safe. We have been with her and her family providing support for most of the day."
Mrs Farquharson said the school counsellor was also involved.
"Our support for the family was immediate and we will continue to do all we can for them over the coming days.
"I held a special assembly today to advise the students of the incident and the importance of walking to school with a friend and also keeping in touch via mobile. The safety of our students is our top priority."
The principal of nearby Newmarket Primary School, Wendy Kofoed, also sent a message to parents yesterday.
She said Newmarket Primary had been informed and warned parents to watch their children.
"If your child walks home along Gillies Ave or in the Alpers Ave, Kipling Rd vicinity we would recommend that you drop your child off at school and collect your child from school until the person is apprehended," she wrote.
An Auckland police spokesman said police had received a complaint about an alleged incident in the area yesterday morning involving an 11-year-old girl, and were investigating. No further details were available last night.
Acting principal of nearby Epsom Girls Grammar School, Karen Smith, said she was aware of the incident but was waiting to hear back from police before commenting further.