Mr Newton said the school's board had already been notified, but there was astonishment yesterday when he told staff and pupils.
St Clair is one of Dunedin's largest primary schools.
"The hardest part was speaking to the staff today. They didn't see it coming.
"The feedback I've had from a couple of colleagues is that it has been very much a surprise.''
His resignation will take effect from September 23, the end of term 3 this year.
Mr Newton said he had been a principal for 27 years, 17 of them at St Clair School, and he felt it was time to find new challenges in life.
"It's been a wonderful place to be and I'm not leaving with any sense of sadness.
"The place has a vibe about it, a dynamic which is very compelling.
"But there's something in me that says it's time for me to do something different with my life.
"I can't quite put my finger on it. It just feels like it's the right time.''
Mr Newton said he did not have any plans for his future beyond September 23, other than to take a break from working in the busy environment of modern education.
"I'm passionate about education, so I will be back - but not in a principalship role.
"There are lots of different things that go into education. It could be consultancy work, it could be some sort of support role.
"Life's a bit of an adventure. You don't really know what's around the next corner. It could be something totally out of left-field that I haven't thought of.''
He said the decision had come after a long period of reflection.
"St Clair School has been a key part of my life for over 17 years, and during that time I have found my role to be a wonderfully rich mix of challenge and satisfaction.
"Leading such a dynamic and innovative school has been a privilege and an honour.''
Mr Newton said it might seem odd to make his announcement at this stage of the year, but the process of appointing a new principal was complex, and providing plenty of notice for the board was critical for a smooth and effective transition.
"The logic around the timing is it allows the next principal to come in and see the place in operation, rather than come in cold next year and having no idea how this place works."
