It would be open seven days and be surrounded by a 2.4m chain-link security fence with landscaping near the front entrance, off Hamiora Place.
The decision comes after a joint hearing was called in August to hear Transpacific's resource consent application to the Bay of Plenty Regional Council and Rotorua District Council.
Both councils had already approved the proposal with conditions, mainly concerning odour prevention, windblown rubbish, storm water and flood prevention, pest control and landscaping.
However, nine submissions were made to both councils from concerned Ngapuna residents, local iwi and business owners who opposed it.
Ngapuna resident and Tapiata and Hamiora whanau spokesman John Tapiata said plans were under way to appeal the decision.
Mr Tapiata said he believed both councils should have allowed for wider public consultation instead of limiting it to those people and businesses surrounding the site.
"This effects the wider community and the four marae in the area."
Mr Tapiata said he was disappointed a cultural impact assessment had not been carried out.
Independent resource consent hearings commissioner Dr Bruce Graham said the physical effects of the activity could be adequately controlled.
"I would also note that the nature and scale of the activities are no greater than those associated with the previous uses of the site.
"It is also relevant to note, as with other submitters, some of the iwi concerns are based on the mistaken perception that the site will be akin to a rubbish dump," he said.
Dr Graham said he was satisfied "the actual and potential effects of the proposed activities will be no more than minor and that the amenity values and quality of the environment will not be adversely affected by the proposal."
Conditions imposed on Transpacific by the commissioner and councils included the company submitting a detailed landscape and stormwater management plan before work on the site began.
Both councils would also be monitoring the site to make sure consent conditions were adhered to.
Te Kura o Te Whakarewarewa principal Hariata Tapiata said students were shocked to hear a refuse transfer station was being built in Ngapuna.
"Many of our children live in Ngapuna ... one said she didn't know how this could happen and wanted to know who said they could build this on their land?
"They are deeply concerned, this is their land, their marae and their bath."
Ms Tapiata said senior students would write to the district and regional councils asking how it could be stopped.
Transpacific officials were unable to respond to The Daily Post questions.
