Social care providers including children's homes have been given up to a year to identify what they owe workers who were incorrectly paid below the minimum wage for sleep-in shifts.
Employers will then have up to three months to pay workers under a new "compliance scheme", ministers said.
The Government has been warned that a number of children's homes could face closure due to a change in the interpretation of the law on pay for overnight carers.
The Independent Children's Homes Association said a poll of 63 of its members - which include residential homes, residential children's schools and short break or respite services - found a quarter believe their organisations could face closure if they do not get help with back pay for staff which has come about as a result of the change.
The payment of a flat-rate "on call" allowance has been the norm across the sector, but following two employment tribunals, new guidance in October last year recognised that the previous guidance was wrong and the minimum wage should be paid for sleep time instead.
Mencap had estimated that the back pay bill for sleep in the learning disability sector alone is estimated at about £400 million.
The Business Department said in a statement: "HMRC will write to social care employers who currently have a complaint against them for allegedly underpaying minimum wage rates for sleep-in shifts to encourage them to sign up to the scheme. Employers that choose not to opt into the scheme will be subject to HMRC's normal enforcement approach.
"The Government is exploring options to minimise any impact on the sector.
"The Government has opened discussions with the European Commission to determine whether any support, if deemed necessary, would be subject to EU state aid rules."
Earlier this year, the Government waived further penalties for sleep-in shifts underpayment arising before July 26 2017.
Enforcement action for sleep-in shifts in the social care sector was temporarily suspended between then and today.
Shadow health minister Julie Cooper said: "Today's announcement is a betrayal of low-paid care staff by the Conservative Government, which also continues to ignore the crisis they've created in social care.
"It is an outrage that care staff, who are some of the lowest-paid in the country, may now have to wait until March 2019 to get the pay they have earned.
"It shows Theresa May's pledge on becoming Prime Minister to help the lowest paid and those, like care staff, working round the clock, to be utterly hollow.
"The Tory Government must ensure that care staff receive the money to which they're entitled and ensure providers can continue to operate so that vulnerable people can continue to receive vital social care services."
Royal Mencap Society chairman Derek Lewis said: "Despite the Government's stated commitment 'to creating an economy that works for everyone', it appears ready to sacrifice the wellbeing of some of the most vulnerable members of society and place at risk the jobs of people who are among the lowest-paid.
"Today's announcement may help HMRC understand the extent of the liabilities for back pay, but it completely fails to give any reassurance to people with a learning disability that their homes and care are secure and to carers that their jobs are not under threat.
"Three months on from the Government's commitment to seek a solution to the devastating £400 million liability hanging over the sector, there is only the promise of further delay and no commitment, even in principle, to accept responsibility for a liability created by Government changing the rules."
Unison assistant general secretary Christina McAnea said: "This scheme helps no-one.
"The care system is creaking at the seams, and no-one wants to see it plunged further into crisis.
"But without sufficient numbers of care workers and a substantial injection of cash from the government that's exactly what will happen.
"Then elderly people and vulnerable adults will be left with no-one to look after them."
She added: "Care workers who have been paid illegally low wages over many years shouldn't have to go months and months before getting back what they're rightfully owed.
"Ministers knew for years that sleep-in workers were not being paid properly. If they'd stepped in sooner, this mess could have been avoided.
"Unfortunately the voluntary nature of this scheme means unscrupulous employers will now be able to slip through the net and their staff won't get a penny back.
"There's a risk too that firms in other parts of the economy will think that failing to pay the minimum wage is not the serious offence it once was, and that they too might get away with a mere slap on the wrist."
Copyright (c) Press Association Ltd. 2017, All Rights Reserved. Picture (c) PA Wire.