FNDC acting chief executive Colin Dale described the arguments as "emotive".
He said the contracts decision was made after both companies took part in a competitive bidding process and was based on the council's duty to save money where possible. There had been no dissatisfaction with Clean Streams' and CBEC's long service, and acknowledged the company's past leadership role in waste management initiatives, Mr Dale said.
"However the price differential between the tenderers of over $2 million cannot be ignored. The emotive arguments in favour of retaining a long-standing and Far North-based contractor in the mix have to be balanced against the council's fiscal responsibilities to the ratepayer," he said.
Greens spokeswoman Denise Roche said Clean Streams had worked closely with Far North communities on waste minimisation projects and was leaving "big shoes to fill".
The council is hopeful its employees will be picked up by the new contract holder. The FNDC will also work with both companies to ensure a smooth transition of service when the contract comes into effect on October 1, Mr Dale said.
The $4.7 million contract for the southern half of the district has remained with current contractor Waste Management.
Both contracts cover the operation and maintenance of transfer stations and resource recovery centres, recycling, transporting non-recyclable waste to landfills for final disposal and the removal of illegally dumped refuse.