Headmaster Tim O'Connor said the focus of the group was "admirable" but didn't strongly align with the school's plans for the next five years.
"We can't afford to alter our operations and direction to manufacture an alignment, as we would be overcommitting our teachers and drifting away from our primary focus of providing our young men with the best education possible," he said.
Education Minister Hekia Parata said the school's choice was disappointing. "A school with that kind of quality and achievement has a lot to contribute."
One of the principals involved in setting up the cluster, Jill Farquharson from Auckland Normal Intermediate, said the community would carry on regardless.
"Everyone is in it positively. We have some competent leaders and very good schools," she said.
Other schools in the group include Meadowbank School, Newmarket School and about six other intermediates and primaries in the Remuera and Parnell area.
Across Auckland, there are communities in Kelston, Lynfield, Te Atatu, One Tree Hill and the Mid Bays area. Nationwide, there are 29 communities comprising 222 schools.
Communities of Schools is part of the Government's flagship education policy, Investing in Educational Success, announced in January last year.
IES has a total budget of $359 million over four years, and $154.8 million a year once it is fully implemented. Almost half that goes to paying for extra teacher time. Another 42 per cent pays for additional salaries for the teachers and principals involved.
The policy has faced criticism from unions, with changes made before the Post-Primary Teachers' Association would sign on, including dropping terms like "executive principal" and reducing bonuses by up to $10,000.
The primary union, NZEI, are still working through a version of the policy with the Government, saying the initial model was not suited to primary schools or early childhood.
Community project
• Government's new Community of Schools policy has 10 per cent take-up.
• More communities (groups of schools) to be announced in July.
• Schools get extra funding and teacher hours to address achievement challenges.