The Port of Tauranga says a decision allowing it to make way for super-sized containerships has ended a near four-year battle with iwi - but one defiant opponent says his battle isn't over.

Conservation Minister Dr Nick Smith yesterday granted three resource consents to the company allowing it to widen and deepen the harbour to make way for large S-class vessels.

The decision comes after the port company had spent $2.5 million in legal fees on their proposal since lodging resource consent nearly four years ago.

The bid had been opposed by Ngaiterangi, Nga Potiki and Ngati Ruahine in an Environment Court battle in 2011.

An eventual decision to grant resource consent for the deepening was later appealed to the High Court by Ngati Ruahine hapu member Lance Waaka.

The court did not grant Mr Waaka leave to take a further challenge to the Court of Appeal, allowing the minister to finally grant consent.

However, Mr Waaka said he was disappointed at the decision, and was now exploring other legal avenues to continue opposition.

"We haven't given up."

Mr Waaka was especially against the port's plans to remove 32m from the Tanea Shelf, the submarine extension of Mauao (Mt Maunganui), which was sacred to local iwi.

But Port of Tauranga chief executive Mark Cairns saw the court process as being over.

Mr Cairns welcomed the announcement with a sense of relief - but he was also hopeful the decision would lead the way to an improved relationship with iwi.

"It's easy to sit here with the European science and say there are going to be minimal environmental effects," he told the Herald.

"I think I've learned personally more about the mauri that the local iwi place on the harbour - and that's something which I think we need to work harder to acknowledge."

Conditions of the consent require restoration of the pipi beds, creation of an artificial reef and careful placement of the dredged sand in approved locations.

A new trust, with members from local iwi, the port and other stakeholders, is also to be set up.

Mr Cairns said the company would soon begin preliminary stages of the dredging process, expected to continue through the year.

The first stage would cost between $30 million and $40 million and was likely to take six months to a year to complete, depending on the size of the dredger.

The second stage would increase the depth of the channel by 3.3 metres and remove 32 metres of Tanea Shelf to make the channel wider.

Dr Smith said he was "disappointed" it had taken nearly four years for a final decision.

The case was one of the last being dealt with under the old Resource Management Act. Future consents of this type would be determined by the Environmental Protection Authority, rather than the minister, and within nine months, he said.

-Additional reporting APNZ

By Jamie Morton @Jamienzherald Email Jamie