Public Health England (PHE) reversed its guidance on Friday evening which said long-sleeved disposable fluid repellent gowns should be worn when treating Covid-19 patients.
Medical staff in England will now be expected to continue working if they do not have full-length protective gowns.
In other parts of the UK, where health provision is devolved from Westminster control, officials have moved to say there are not the shortages seen in England.
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According to the latest PHE guidance, if full-length gowns are not available clinical staff are advised to wear "disposable, non-fluid repellent gowns or coveralls" or "washable surgical gowns" with aprons.
The guidance adds that staff should wash their forearms afterwards.
The updated guidance states that the "reuse of PPE should be implemented until confirmation of adequate re-supply is in place".
It continued: "Some compromise is needed to optimise the supply of PPE in times of extreme shortages".
Reacting to the news, shadow health secretary Jonathan Ashworth said: "Week after week, we hear of problems in PPE getting to the front line despite what ministers tell us at Downing Street press conferences.
"This ongoing failure needs fixing and ministers must explain how they will fix it urgently."
A Department of Health spokesman said: "New clinical advice has been issued today to make sure that if there are shortages in one area, frontline staff know what PPE to wear instead to minimise risk."
Dr Rob Harwood, consultants committee chairman at the British Medical Association, said the change in guidance asks medical staff to "put their own lives on the line.
"Telling staff to use aprons in the place of gowns directly contravenes both Public Health England's previous guidance and that of the World Health Organisation.
"This is guidance that's there to help keep healthcare workers and their patients, out of harm's way.2
He added: "Too many healthcare workers have already died. More doctors and their colleagues cannot be expected to put their own lives on the line in a bid to save others, and this new advice means they could be doing just that. It's not a decision they should have to make."
Saffron Cordery, deputy chief executive of NHS Providers - which represents hospital trusts - said some trusts could run out of gowns this weekend.
Ms Cordery added this was despite trusts "carefully managing" remaining stock and collaborating with neighbouring health organisations where possible.
She said: "We all hope that this temporary disruption to supply will be short-lived and that the gowns that were ordered a long time ago, and should have already arrived, start arriving consistently and reliably rather than in the current fits and starts."
Mr Hancock told the Commons Health and Social Care Committee that the equipment was a "precious resource" and that maintaining supplies was challenging due to the very high global demand.
The shortage is not across the whole UK, with the Welsh government issuing a statement on Friday night saying it is "keen to reassure everyone it has PPE stock and we currently do not anticipate any disruption to supply. We therefore do not expect this alert to be enacted in Wales at the present time.
It continued: "We are working hard to procure PPE and we are receiving huge numbers of offers from Welsh businesses willing to help with PPE supply and have several large-scale production projects underway."
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