In a letter to the council about the application, Parker said he would direct the council to consult with the Tauranga Moana Iwi Collective and the Hauraki Collective.
"I consider that consultation with the above groups is necessary given the relationships and interests in the area."
Bay of Plenty Regional Council chief executive Fiona McTavish wrote back in January asking him to reconsider including Hauraki.
"BOPRC has serious reservations in regards to the requirements to consult with the Hauraki Collective."
She said council staff previously raised concerns with Office of Treaty Settlement officials about the "precedent risk and implications of consulting iwi with no recognised relationship with the subject locality."
"Our understanding is that the nature and extent of Hauraki iwi representation on any Tauranga matter is still to be determined, especially given recent Waitangi Tribunal urgency proceedings and public displays of conflicting iwi views regarding mana whenua in the Tauranga area," McTavish said.
Ngāi Te Rangi have argued Hauraki's settlement would give the collective mana whenua level cultural authority in Tauranga.
Iwi chief executive Paora Stanley the letter looked like the Government putting pressure on the council to "jump ahead of legislation" that had not gone through.
"It's not right."
Parker told the Bay of Plenty Times the direction he gave the council "did not signal a Crown view, or otherwise, on mana whenua status in the Tauriko West area".
He said he changed his mind after hearing the council's views and talking to Treaty Negotiations Minister Andrew Little.
Little said he was satisfied the direction did not pre-empt Hauraki options.
"The options available will remain further down the Resource Management Act process."
Pare Hauraki negotiator Paul Majurey said Hauraki's role and ties to Tauranga Moana had been confirmed after extensive consideration by the Waitangi Tribunal.
"They found Hauraki iwi occupied land, fished and gathered resources in the northern part of the Tauranga region; they established kainga, named places, fought and reached agreements with their neighbours; they died and were buried there."
Relations between the two collectives - Tauranga Moana and Hauraki - have been strained by the latter's prolonged settlement process.
Ngai Te Rangi has led a series of public protests - including a dawn protest at the Hauraki boundary this week and a 400-person hikoī to Parliament in May - calling for the Crown to step back and let the groups sort out their cross-claims through tikanga without time constraints.
