Care homes may be forced to close and thousands of staff risk losing their jobs if they decline to receive their first Covid-19 vaccine by the end of Thursday, ministers have been warned.

Providers and unions have warned of an exodus of staff in England due to the government’s requirement for them to be fully vaccinated against coronavirus by 11 November. Thursday has been set as their last opportunity for a first dose unless they are medically exempt.

Andy Burnham, the mayor of Greater Manchester, said the mandatory vaccination policy was “very unfair” and that about 2,000 of the region’s care home workers faced losing their jobs overnight unless they received their first jab within hours.

Burnham said carers were being “singled out” by the government, although the health and social care secretary, Sajid Javid, has said that the policy was “highly likely” to be extended to frontline NHS staff after a consultation.

Ministers have previously said they estimate that about 7% of the 570,000 CQC-registered care home staff in England – about 40,000 people – will refuse the vaccine and therefore no longer be able to care for residents after 11 November.

Prof Martin Green, the chief executive of Care England, a body representing independent care service providers, said the policy would deepen the sector’s staffing crisis and could force some homes to close.

“We all accept we want as many people as possible to be vaccinated. But I do feel the government has gone forward with the social care compulsion without understanding the implications, without having a thought-out plan on how they are going to deal with staff shortages,” he told BBC Radio 4’s Today programme on Thursday.

“Care homes are now in a difficult position, facing the reality of do they have enough staff to maintain safety and quality of care? They are in the position of either having to transgress the law or expose people they support to levels of staffing that are not going to deliver the safety you’re required to.”

He added: “There’s the inevitability that in some areas, if you can’t get the staff, then there will be care homes that close.”

North Yorkshire council said about 400 of its 20,000 care sector staff had not yet received a vaccine, meaning they risk losing their jobs.

Burnham said about one in 10 of all health and social care staff in Greater Manchester were not vaccinated, including about 2,000 care home workers.

“It’s for different people to make their judgments about the vaccine but I do believe it’s very unfair to put people in a position where they have concerns but then have no ability to maintain their job, if they’ve chosen not to be vaccinated,” he said.

“It is the case also that staff are leaving social care to work in the NHS where there is no such restriction, so it’s hard to see the logic of this particular policy when it doesn’t apply more broadly. Either it shouldn’t apply at all, or it should apply more broadly.”

A Department of Health and Social Care spokesperson said: “Over 90% of care home staff have received their first dose of a Covid-19 vaccine ahead of the 11 November deadline and we encourage even more staff to get vaccinated to protect their colleagues and those they care for.

“Temporarily, those who meet the criteria for a medical exemption will be able to self-certify until we introduce a new system. This will ensure those with medical exemptions can continue working in care homes.

“Our message is clear: vaccines save lives and it is our responsibility to do everything we can to reduce the risk for vulnerable people in care homes.”