"There are a number of companies producing manuka honey with different statements and claims. MPI is acting to ensure that manuka products are true to label and not misleading customers."
The guideline is available to the public and includes points on how to identify a food as having New Zealand manuka-type honey.
Some of the characteristics that manuka honey should have include the presence of manuka-type pollen, an earthy and aromatic smell and a slightly bitter taste.
Producers have also been warned to be careful about what they include on labels, such as health claims and statements such as "a product of New Zealand" or "100% New Zealand".
For those statements to be included, the product must have originated from New Zealand and all or virtually all processes involved in its production or manufacturing carried out here.
Brett Hewlett, head of Comvita, the country's largest producer of honey, praised the ministry's move because it helped to reel in "the cowboys" who ruined it for the rest in the industry.
"The majority of New Zealand producers are doing a great job ... but we've got some cowboys operating on the fringes and this is a good start to try and fix that issue."
Food Safety Minister Nikki Kaye said that such a labelling system helped to regulate the product, which is in high regard, particularly overseas.
"It's important that New Zealand takes this step to protect our brand and the integrity of our labelling systems," she said.
The guidelines - which will be validated with more research findings next July - was put together following consultation with people within the honey industry as well as scientists.
Mr Gallacher said the ministry would carry out ongoing and random testing on honey products to ensure manufacturers were being truthful.
They would also continue their scientific research by using emerging technologies to detect even more aspects that differentiate manuka honey from others.
Read the interim labelling guide here: