He said being placed in a low streamed class could impact a learner's self-esteem and "narrow their educational pathway".
"To stream a boy based on what happens coming out of Year 8 sometimes can condemn them to have low belief and low self-esteem," he said.
"That impacts upon their aspiration to achieve their educational goals.
"Through mixed ability, we are hoping they can all be inspired to achieve their academic potential."
School staff had spent the past 18 months reflecting on research for and against the practice, with most evidence "strongly in favour of doing away with streaming".
The school's board and staff supported the move.
Mangan also believed the mixed-ability model would allow students at different learning levels to help each other.
He said teachers who were not familiar with the model were set to undergo professional development.
"The teacher has to grow an understanding on how to differentiate the delivery of the curriculum to be ensuring each of those different levels are developing."
John Paul College principal Patrick Walsh said there was no "strong evidence" that streaming benefitted any students - including top academic performers.
And he said negative impacts of streaming were "amplified" and "long-lasting" for Māori and Pasifika learners.
"This is inconsistent with our Catholic worldview and commitment to being culturally inclusive.
Walsh encouraged other schools to review the research and consult their communities about class streaming.
For junior students at Ōtūmoetai College, classes were grouped into three areas for core subjects.
While the majority of students were in mixed ability classes, principal Russell Gordon said those with "additional learning needs" and "gifted and talented" students were separated.
Numbers were a "little lower" in learning support classes, whereas extension classes were for students "outperforming" in core subjects.
Gordon said this helped ensure all students were able to "reach their personal best". It also meant in mixed classes teachers were not trying to meet the needs of students across a wide range of curriculum levels.
"These classes are not homogeneous, but the variation isn't as great.
"I can be more confident that the teacher can divide learning so that it better meets the needs of individual students rather than teaching to the average."
Ministry of Education group manager policy Tipene Crisp said any move towards "more inclusive and equitable learning environments" was supported by the Government.
Crisp said there was "clear and consistent" evidence that streaming contributed to inequitable outcomes, particularly for Maōri, Pacific and learners with disabilities who were placed in lower streams.
"We recognise that collaboration is needed between the education sector and communities to develop solutions to support this shift."
The ministry was supporting this by including "more inclusive local curriculum design and the development of culturally responsive and collaborative teaching practices".
These supports focus on helping schools develop more inclusive and equitable education practices, including moving away from streaming and ability grouping in the classroom, especially for Māori and Pacific students.