The college's president, Samantha Murton, said it had been "extraordinarily difficult" to get more and that was leaving doctors in the community vulnerable.
It was highly likely a GP could encounter the first case in the country and that could happen at any time, she said.
"Sometimes the hospital sector doesn't recognise that patients just rock up to us without telling us that they're coming in. So, we need the gear straight away," Dr Murton said.
The ministry had done a stocktake of what clinics had and made a commitment to releasing some of the masks, she said.
"But GPs feel it should be now - not waiting for the first case to turn up in New Zealand. We need to be guarded when that happens," she said.
The lack of protection could not only make doctors vulnerable to catching the disease but threaten healthcare for the many patients they would need to care for if the disease spreads, she said.
The ministry's director of public health, Caroline McElnay, said it was important general practices had the level of protective equipment they required.
It was working with local health authorities to ensure they were supplied, she said.
The ministry also had a plan to set up community-based assessment centres to take the load off GP clinics if there was an outbreak of Covid-19, Dr McElnay said.
She urged New Zealanders to get a flu vaccine to take the load off the system should the novel coronavirus coincide with flu season.
Morton said the College of GPS had been working closely with the ministry, and a few doctors' practices had been contacted by District Health Boards offering masks, but so far there was no obvious answer on how to get more equipment. "It's just that next step that has to happen really fast for us."
- RNZ
