Backed by the wider honey industry and government, The Mānuka Honey Appellation Society has been working to protect the term so that only honey from New Zealand can be called mānuka since 2015.
It argues mānuka is a Māori word and a distinctive product of New Zealand.
But the Australian Manuka Honey Association has been appealing the effort in multiple markets - saying honey produced there can also be called mānuka.
In a decision released on Monday, the Intellectual Property Office of New Zealand found the society's certification mark bid did not meet necessary requirements.
"This case represents a trans-Tasman tussle of extraordinary proportions over trade mark rights for mānuka honey. It is one of the most complex and long running proceedings to have come before the Intellectual Property Office of New Zealand," the ruling said.
It ordered the society to pay the Australian Manuka Honey Association costs of $6430.
In 2021, the United Kingdom rejected a bid by the Mānuka Honey Appellation Society to trademark the term 'manuka honey' in the UK.
But the society vowed to continue its fight and earlier this year refiled court proceedings in the UK and European Union.
The Australian Manuka Association welcomed the New Zealand trademark win saying it was a "common sense outcome" which paved the way to accelerate global sales.
Chairman Ben McKee said the group was delighted with the judgement.
"It confirms what we have been saying since New Zealand producers began this legal process nearly eight years ago - our product has a long history of being recognised as Manuka honey, it is produced like the New Zealand product is, and it also offers the sought-after antimicrobial properties that consumers around the world value so highly," he said.
McKee said the decision ensures Australian beekeepers can fairly market their produce, and the term Manuka honey was a descriptive term.
"The fact that even authorities in New Zealand cannot find a way to support the trademark claims of New Zealand producers should, we hope, bring this legal dispute to an end once and for all," he said.
McKee said it was only a particular group of New Zealand producers, under the umbrella of the Manuka.
Honey Appellation Society (MHAS), which had spearheaded the trademark campaign, and other New Zealand beekeepers and industry members who were prepared to work more collaboratively with the Australian industry.
The New Zealand based Mānuka Charitable Trust said it was disappointed but undeterred by Intellectual Property Office ruling on mānuka honey.
"Today's finding reflects the technicalities and limitations of conventional IP law to protect indigenous rights. It is disappointing in so many ways, but our role as kaitiaki (guardians) to protect the mana, mauri, and value of our taonga species, including Mānuka on behalf of all New Zealanders is not contestable," Manuka Charitable Trust chair Pita Tipene said.
"We remain resolute in protecting our reo Māori (language) and the precious taonga (treasure) and today's ruling in no way deters us. If anything, it has made us more determined to protect what is ours on behalf of all New Zealanders and consumers who value authenticity. We will take some time to absorb the details of the ruling and consider our next steps," Tipene said.
Industry partners also remain steadfast in their resolve the Mānuka Honey name belongs and should refer only to products produced in Aotearoa New Zealand.
The lack of recognition of indigenous rights in the intellectual property regime is well established both in New Zealand and overseas, Tipene said.
"It is time the New Zealand government took urgent action and committed sufficient funding to address these issues as raised in the Wai 262 claim and recognised in the United Nations Declaration on the Rights of Indigenous Peoples," he said.
