Urgent-care and after-hours medical clinics say they're "on the brink of collapse" and will have to cut hours and staff unless they get urgent funding.
And general practices say previously promised funding being withdrawn could be life-threatening for frontline health services amid a "war against Covid-19".
Dr Kate Baddock said during the month of lockdown deferred co-payments at her Warkworth Medical Centre had stacked up to $40,000.
For the same period the month before, co-payment debts were $500.
The issue was patient numbers had been decimated as people stayed home and many were no longer able to afford consultation fees, she said.
Baddock couldn't speak to her total overheads but said staffing costs alone were about $80,000 a month.
"GPs are in crisis, we really are."
Other GPs across the country would be in similar - if not worse - positions, Baddock said as her practice was a Very Low Cost Access clinic where charges were capped at $19.
Practices of a similar size but which had higher fees would likely have even worse debt, she said.
"We don't know if that's bad debt because people can't afford to pay, through no fault of their own, and if we'll never see that money again or if it's deferred.
"Either way, our cashflow has totally dried up."
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And while they're buckling down to cut costs, Baddock said they also had to prepare in case there was a deluge of patients after the lockdown.
Dr Peter Boot, from Northcare Accident and Medical on Auckland's North Shore, said he had kept the doors open for more than 10 hours a day, but it had come at a cost.
The $22.5 million funding package which was distributed on April 10 was paid based on how many patients practices had enrolled.
This meant urgent-care clinics, which don't have many enrolled, missed out on a lot of the funding.
Boot said his staffing costs alone could be $1000 an hour so they would need 60 patients a day just to pay the bills. The wage subsidy scheme wasn't enough to really help as there were a lot of other bills which came with staying open, he said.
During the lockdown, Boot said they got up to just 12 people a day.
"The slow demise of general practice has been like a tectonic plate slowly grinding against its neighbour," he said.
"The Covid crisis will be like an earthquake, hastening changes and the demise of GP services as we've come to expect them. It's ironic that this should occur when the country is so reliant on its medical workforce."
Northcare Accident and Medical had become a Community Based Assessment Centre (CBAC) for Covid-19 which had provided a small funding relief, Boot said.
Accident and Medical Clinic Association chairman Neil Beumelburg said urgent-care practices were being pushed to the brink of collapse.
"If clinics are not supported now they will not be well placed and ready to deliver care to people who need it, including those people most at risk.
"That will also result in a tsunami of unmanageable demand arriving on the doorsteps of hospitals and their emergency departments."
Baddock said a miscommunication over a second tranche of funding led to practices making business decisions to help survive the crisis which they had to now reconsider.
On April 9, there was some relief when the Government agreed to a $22.4 million package to keep GPs afloat.
That came on top of the $15 million which had gone to reimbursing clinics for set-up costs to prepare for Covid-19.
When it was approved, lead District Health Board chief executive Nick Chamberlain emailed health boards and Public Health Organisations saying a $45 million package had been approved and would be split into two payments.
"There will be a second identical payment in two weeks' time to ensure that the financial impact to general practices of the first four weeks of the lockdown have been covered," Chamberlain said in the email.
But it's understood the second tranche of $22.4 million was never signed off by Cabinet and a miscommunication somewhere in discussions led to the promise there was more to come.
It's not clear where in discussions the miscommunication happened.
Health Minister David Clark said in a statement the Ministry of Health was providing advice to Cabinet to ensure there was "an appropriate process" to consider all funding requests from the health and disability system.
That process would take into account all providers across the board such as pharmacy, aged care, disability services, family planning, maternity and hospices.
The Ministry of Health has previously said the funding was part of an "ongoing discussion".