Distribution of some gloves has also been suspended because they may not meet technical requirements.
The Department of Health told the BBC safety of frontline staff was an absolute priority.
Its warning is related to the specific FFP3 brand, which are more sophisticated than surgical masks.
They are worn in intensive care or when certain procedures are carried out that can generate aerosols – tiny virus particles that can build up in stuffy rooms and have been linked to outbreaks of Covid-19.
Last month, the British Medical Association appealed for staff on general wards to be given this type of mask to guard against coronavirus infection.
The Department of Health and Social Care’s alert last week warned that a certain type of FFP3 – branded “Fang Tian” and marked as FT-045 – may not meet the required technical specifications.
It advised health and care providers to check to see if their stock included the product and to stop using them until further investigation.
The alert said the masks were provided by Polyco Healthline, but the manufacturer Suzhou Fangtian Industries told the BBC it had never supplied the firm.
Polyco Healthline was approached for comment by the BBC but has not yet responded.
A DHSC spokesman said the affected 12m masks was about four per cent of overall stocks.
He added there was a “resilient supply” of FFP3 masks to ensure staff had access to the PPE they needed.
The department also issued an alert about “nitri-hand” non-sterile nitrile examination gloves – 27 million of these have been supplied by Full Support Group since June last year.
The packaging for the gloves is understood to say they had not been tested for resistance to virus.
But the supplier, Full Support Group, said they had in fact passed the test and the packaging should have been amended.
“We are confident that the gloves in question, having been checked and confirmed that they meet the requirements, will be released from quarantine as soon as the administrative process has been completed,” a spokesman from the supplier said.
He added that Full Support had successfully supplied the NHS since 2002.
The DHSC said the batch of gloves represented a very small proportion of overall supply.
Rob Harwood, BMA consultants committee chairman, said it was “unacceptable” if staff safety is still being jeopardised by inadequate PPE a year into the pandemic.
He said: “Healthcare staff working on the frontline do so facing the grave risk of contracting Covid, and deserve the best protection from this deadly virus.
“Many will be incredibly concerned to learn that some masks designed to offer enhanced protection, as well as gloves, may not meet standards, potentially placing them at greater risk.”
He said it was “good” to see immediate action but “urgent clarification” was needed to explain “how they entered the supply chain”.
The Department of Health and Social Care said: “Our priority is providing frontline staff with quality PPE that meets robust quality requirements, and we have delivered nearly eight billion items so far.
“We carry out extensive due diligence on all PPE items before release, and where an issue is identified we act quickly to isolate the relevant product and conduct the appropriate investigations.”