Grow Rotorua chief executive Francis Pauwels said the deal was important for landowners and water quality.
He said farmers in the Lake Rotorua catchment had a big task ahead to meet restricted nutrient rules by 2032 and they needed solutions now.
A $45.5 million land-use incentive fund for landowners has been set aside by the Bay of Plenty Regional Council.
The funding is awaiting approval by the government and is expected shortly.
"Grow Rotorua has a mandate to grow the primary sector by identifying alternative land-uses for landowners," Mr Pauwels said. "Manuka honey, oil and tea have been identified by Grow Rotorua as one of these alternative land-uses.
"Pastoral farming will still have a large role in the Rotorua catchment, but to meet the proposed nutrient limits we need other options on the table.
"Manuka plantations can potentially be a really good option for farmers but there are no existing plantations around Rotorua.
"We need to get manuka plantations in the ground and growing, so we have the numbers to back up the proposition."
New Zealand is the only country that produces the internationally-recognised Unique Manuka Factor (UMF) manuka honey. It is a valued export at about $120 million and is forecast to eventually become a billion dollar industry.
The Pudneys are planning to plant 37ha of their Hamurana farm in manuka this winter.
"A lot of the focus has been on the cause of the nutrients but, as a landowner and a farmer, we now need solutions like apiculture so that's why we are trialling it," Mr Pudney said.
"We also need to know what financial help will be available. Until the incentive funding is approved, it just adds to the uncertainty.
"There is so much uncertainty in the Rotorua farming community right now. There are some farmers seriously questioning whether there is a future in farming with the restricted nutrient limits coming in."
Costs to convert pastoral land to manuka plantations are about $2000 per hectare and it takes at least three years before any significant honey collection occurs.
Comvita chief executive Brett Hewlett said the company had been in discussion with Grow Rotorua for the past six months and was keen to include Rotorua in the nationwide programme.
"This programme will provide important information to create a viable new land-use for New Zealand and help grow manuka honey exports," Mr Hewlett said.
"Gathering this information is only possible with the landowners coming on board and we're incredibly grateful to everyone who has agreed to participate in the research.
"It would be great to have Rotorua landowners join the 23 established commercial trials on 700ha across New Zealand."