Under-Secretary to the Minister of Education, David Seymour, said Ms Whaitiri demonstrated a complete misunderstanding of the policy by suggesting a partnership school application should be screened by a local principals' association.
"There is no requirement for principals from schools to be consulted before a partnership school is approved. Partnership school applications are evaluated by an independent authorisation board."
Stephen Hensman, chair of the Hawke's Bay Secondary Principal's Association, said they were shocked that the local Ministry of Education office was also left in the dark.
"The local Ministry of Education was just as surprised as us and the local knowledge available by both the office and local schools had not been treated as the rich resource it is."
He said because they were not consulted they had been unable to conduct discussions about how the current concerns for Maori boys could have been addressed within the existing network.
"We are passionately involved in helping Maori boys be successful, which is why we are so disappointed."
Ms Whaitiri said: "If Hekia Parata was genuine about raising educational outcomes for young Maori men in Hawke's Bay, then the first step should have been to draw on the experience of our local network of schools and principals to identify the issues and develop solutions."
Mr Seymour said Te Aratika's application was supported by data on rates of Maori educational underachievement and disengagement in the region, and evidence of the potential demand for a school of this type.
Tukituki MP Craig Foss said he supported any move to get better outcomes for those students who for whatever reason were under performing or perhaps not even attending school.
"We have some really challenging social issues across Hawke's Bay. This is an opportunity for our young people, particularly young Maori, to succeed. If we do what we've always done, we'll get the same failed outcomes. Why wouldn't we try something different?"
Mr Hensman was also concerned that the charter school was being aimed at students who were succeeding in mainstream with an open enrolment policy.
"This is strange as Ngati Kahugnunu Inc endorsed the charter school as a way to reverse the negative trajectories of some of our most at-risk rangatahi, not to target those who are already succeeding and thriving."
Mr Seymour said if families seek to enrol students in a partnership school, which passed the application process, that was their right.
"The views of the local principals' association do not negate families' right to educational choice."
Mr Seymour said the Ministry of Education made contact with all schools in Hawke's Bay to inform them about the new school after he announced its approval to open.