It has asked district health boards (DHBs) not to use them it while it checks they're up to scratch and gets more information from suppliers.
It said it does not mean the masks are non-compliant.
The MOH said the masks are N95 and procedure masks.
Kate Weston, from the New Zealand Nurses Organisation, said it had prompted fears hospital staff were working in unsafe conditions.
"We need to know our members - health care workers, nurses, midwives, health care assistants and other health professions - are actually safe at work.
"It is a health and safety issue."
The MOH said New Zealand continued to have a sufficient supply of PPE; national stores and DHB reserves held 50 million masks, and it said another 90 million masks were on order.
RNZ asked the MOH whether it had quality concerns about the 90 million masks on order.
It said steps were being taken to improve policies and procedures for securing PPE.
Faulty products costing governments millions
Infectious disease expert Siouxsie Wiles said there was a massive problem worldwide with countries buying defective Covid-19 protective gear and testing equipment.
Wiles said faulty equipment had cost governments a fortune.
"There are inferior products on the market and because everybody is clamouring for the same thing.
"Because there is a worldwide need for PPE, for kits of every resource, that people are ending up spending millions and millions and millions of dollars on things that are not fit for purpose."
Cause of non-compliant masks entering New Zealand
The NZ Occupational Hygiene Society (NZOHS) said a shortage of disposable respirators, also called "dust masks", caused by high global demand during the Covid-19 pandemic, had led to non-compliant masks entering New Zealand.
NZOHS president Carol McSweeney said the non-compliant masks put workers, including construction and manufacturing workers, at risk of inhaling dust, fibres, fumes and other contaminants that could seriously harm their health.
"It's essential that businesses buying respirators for their workers, or retailers buying them to on-sell, know how to identify genuine masks," McSweeney said.
"Otherwise they may be buying masks that claim to provide protection that is not actually there.
"Signs a respirator is not compliant include it having no markings to identify the safety standard it meets, no manufacturers' name or logo, no references to certifying bodies and unusual designs."
WorkSafe in May issued an alert about non-compliant respirators entering the country.
