Funding to desperate general practices for the second half of lockdown has been blocked by the Government.

It comes as GPs brace for a "tsunami" of patients who'd put off seeing a doctor and pulling the rug on the payment could see some practices financially compromised, says the primary care sector.

The Ministry of Health said the $22.4 million package was part of an "ongoing conversation" with the sector and the Government.

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GPs are an essential frontline health service but have come under mounds of financial pressure as appointments dried up, which has drastically impacted their incomes

Practices can access the wage subsidy scheme, but that has to be paid in full to their staff.

They've also had the costs of moving to virtual appointments and other infrastructure needs to ensure they could operate safely during the Covid-19 pandemic.

The Government has paid out $15 million for those costs and further $22.4 million to help practices stay afloat.

Payments were worked out at $2.34 per patient for urban practices and $2.46 for rural practices. This amounted to thousands for some GPs.

An email from a District Health Board chief executive on April 9 announcing the first payment said there'd be "a second identical payment in two weeks' time" to ensure that the financial impact of the lockdown was covered.

It was based on $45 million over four weeks.

But the second $22.4 million payment has since been blocked.

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Auckland Public Health Office ProCare told its members Cabinet didn't approve the payment.

"The rationale given is that the Government needs to get to grips with the scale of the economic disruption caused by the shutdown; for both essential services and those who have had to close during the shutdown, beyond the health and disability sector."

ProCare told its members they were surprised and disappointed with the decision and were continuing to negotiate for the funding.

Dr Tim Malloy, chair of GenPro which represents GP owners, aid the funding U-turn was a massive blow to already desperate GPs. Many of them had already allocated that money to cover upcoming staffing costs and ensure they could maintain their levels of service.

"These are overheads which have literally already been spent," said Malloy.

"From my perspective, the message it sends is that we're not valued."

One practice told the Herald they were depending on the second payment and without it would have to ask staff to work reduced hours and cut other costs.

Malloy said the blow came just as practices were preparing to catch up on healthcare that had been put off during the lockdown.

"It's a double-whammy. We're waiting for the tsunami of healthcare that's been put off for the last six weeks or so and we're trying to prepare so we're capable and in a good position to prepare for that.

"And then to have this annoyance come along and really just compromise what you're doing is really unhelpful and makes it that much more difficult for planning.

"We really don't need this."

Malloy wants Cabinet to urgently reconsider the decision.

"It's also a distraction from our real work, which we don't need. There's enough to be doing out there anyway.

"It's wrong on so many different levels."

Director General of Health Dr Ashley Bloomfield said the funding hadn't been taken away but the conversation was ongoing.

"There is an active conversation between the Minister and General Practice leaders and the Ministry on further funding so that's ongoing and I can't comment any further on that."

Medical director at the Royal New Zealand College of General Practioners, Dr Bryan Betty, said they'd had no indication the second $11 million payment would come through in the near future.

Practices in high needs areas were especially struggling and there was an expectation there would be more funding, he said.

"We absolutely would like to see this decision revised."