"One of our key concerns is that the small communities of Northland will be dwarfed by Auckland because of its size," Kaipara Mayor Dr Jason Smith said.
The three waters needs of 180,000 Northlanders would get lost among those of Auckland's 1.75 million residents, Smith said.
Northland's councils' preference was instead for a regional Tai Tokerau approach. They were already working well together regionally, a key requirement for being able to access the Government three waters restructure money.
But that regional work could be across Northland rather than inter-regionally with Auckland Council, Smith said.
The Government money, announced on Tuesday, would give the FNDC $5.90 million, WDC $5.89m and KDC $2.35m.
They have until August 31 to sign a memorandum of understanding to get these individual allocations.
There's also $14.13mfor the councils to work together to amalgamate drinking water, wastewater and stormwater infrastructure and provision in the region. They have until September 30 to decide among themselves who gets what from that money.
New Zealand's biggest three waters review aims to slash the country's 67 three-waters providers to half a dozen or fewer. It comes after up to five people died and 5000 people became sick in 2016 through campylobacter contamination of Havelock North drinking water.
Smith said KDC would decide whether to sign the memorandum, and therefore be able to get the money, at its August 26 meeting. Ann Court, FNDC deputy mayor said her council also had yet to decide whether to opt in to the restructure. Staff were urgently preparing an options report for councillors to consider before the August 31 deadline.
Councils must specify infrastructure projects and their timelines before getting their money.
The Government allocations are based on councils' population and geographic size They are expected amounts, rather than being set in stone.
The Government has also put up $30 million for non-council rural drinking water suppliers.
Nanaia Mahuta, Minister of Local Government said this helped address challenges these supplies faced in delivering safe drinking water. "There are a range of private supply arrangements in rural and remote areas," Mahuta said.
"Affordability challenges are particularly acute for some non-council drinking water suppliers including marae," she said.
Brian Hanna, three waters steering committee independent chair, said Northlanders' future access to safe drinking water was under threat without major spending on infrastructure that only bigger management organisations could afford.
"There's a risk of failure to meet safe drinking water standards, with potentially serious consequences for public health, the environment and the economy."
Millions of dollars was needed to maintain and upgrade Northland's infrastructure for safe drinking water, wastewater and stormwater into the future – part of as much as $574m needed nationally.
Hanna helms the local and central government committee with a key role in making the industry shakeup happen. He was in Northland recently as part of a nationwide 12-centre roadshow.
About 30 people, including Northland mayors, council chief executives and managers attended a workshop in Whangarei.