A spokesman for Prime Minister Theresa May said disposing of the documents was the right decision to take, amid a row over the immigration status of people who came to Britain from the Commonwealth after the Second World War.
Labour MP David Lammy said “heads must roll” at the Home Office, while shadow home secretary Diane Abbott labelled the revelation “truly shocking”.
The Home Office, which took the decision for data protection reasons, said the slips “did not provide any reliable evidence relating to ongoing residence in the UK or their immigration status”.
The PM earlier told Caribbean leaders she was “genuinely sorry” for the “anxiety caused” and said she wanted to dispel the notion that the Government wanted to clamp down on citizens from the region.
Named the Windrush generation after the cruise ship that brought one of the first large groups of West Indians to Britain, anyone who entered the UK before 1973 is legally entitled to live in the country.
However, despite having been in the UK for the majority of their lives, the group of British residents have begun to experience issues as a result of tightened immigration requirements.
It has seen some Windrush generation residents, who might never have felt the need to apply for a UK passport before, left without the documentation now required by officials.
As many as 50,000 are thought to be experiencing difficulties in finding work, getting NHS care, accessing benefits, or trying to secure housing.
There are even fears some may have been deported in error.
Home Secretary Amber Rudd has said she did not have “any evidence” this had happened, but Cabinet Office minister David Lidington said on Tuesday that officials were trawling through files to establish whether there had been any wrongful deportations.
On the subject of the registration slips, the PM’s spokesman said the UK Border Agency disposed of them in 2010, which is when Mrs May was in charge of the Home Office.
He said: “The slips provided details of an individual’s date of entry, but did not provide any reliable evidence relating to ongoing residence in the UK, or their immigration status and therefore would not have bearing on immigration cases whereby Commonwealth citizens are proving residency in the UK.”
He added: “It was done for, I think, reasons as well to protect personal information.
“The decision was taken to securely dispose of these documents, and that was the right one to take.”
When asked if Mrs May had been aware of the disposal when she was home secretary, the spokesman responded: “My belief, at this moment, is that it was an operational decision that was taken by the Border Agency.”
Reacting to the disclosure, which was first reported by The Guardian, Mr Lammy tweeted: “It is an absolute disgrace that the Home Office has destroyed these documents and then forced Windrush-generation migrants to try and prove their status, threatening them with deportation and stripping them of their rights. Shame on you all.”
It is an absolute disgrace that the Home Office has destroyed these documents and then forced Windrush-generation migrants to try and prove their status, threatening them with deportation and stripping them of their rights. Shame on you all. #Windrushhttps://t.co/ccIFryoLXB
— David Lammy (@DavidLammy) April 17, 2018
Ms Abbott said culpability for the “fiasco” rests with the Home Office.
She added: “Amber Rudd must explain who authorised this action and when, and what Theresa May’s role was as the then Home Secretary.
“The Windrush generation have been threatened with deportation because they cannot provide documents, but now we learn that the Home Office destroyed the very records that could have demonstrated their right to remain.
“The Home Secretary should immediately announce that she will accept the burden of proof in deportation cases like these lies with the Home Office, not with the potential deportee.
“And she should say what steps she will take to ensure that people who have a right to be here continue to enjoy free access to the NHS, and the freedom to change jobs, homes or bank accounts without further harassment under her Government’s hostile environment policy.”
A Home Office spokesperson said: “Registration slips provided details of an individual’s date of entry, they did not provide any reliable evidence relating to ongoing residence in the UK or their immigration status.
“So it would be misleading and inaccurate to suggest that registration slips would therefore have a bearing on immigration cases whereby Commonwealth citizens are proving residency in the UK.”
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The department stressed that when deciding immigration cases officials consider alternative evidence, such as tax records, utility bills and tenancy agreements, as evidence of ongoing residency in the UK in these exceptional circumstances.
:: The Home Office has set up a dedicated web page to help Commonwealth citizens confirm their status in the UK, which can be found here. Alternatively, call the Home Office helpline on 0300 123 2241.