The upgrades are due to be completed by 2020.
As well as the hospital at Rawene, the trust operates 10 GP clinics throughout the Hokianga plus a maternity service and healthy living programmes.
The Hokianga is one of only a few areas in New Zealand where all primary health care is provided free of charge. The other area is Whangaroa.
Comvita chief executive Scott Coulter said the company saw benefits in partnering with like-minded organisations in the communities it operates in, and the trust's focus on hauora and holistic wellbeing aligned with Comvita's values.
The company had operated an apiary business, Kiwi Bee, out of Northland since 2008, and co-founder Claude Stratford lived in Northland in the late 1960s and early 1970s as a beekeeper.
''Our business has close ties to Northland and we want to play our part in contributing to the local community," he said.
As to why the company specifically singled out Hokianga Health, spokeswoman Emma Schuler said the company had been impressed by the trust's model, and thought it could be replicated around New Zealand.
Comvita has a number of hives in the Hokianga and likes to give back to communities where it operates.
Representatives of both parties marked the agreement by planting a mānuka seedling at the hospital grounds in Rawene.