The unidentified man was waiting to be processed at the Manston centre, which has been criticised for what NGOs call "inhumane" conditions.
A man who arrived in the UK on a small boat about a week ago has died after falling ill at a migrant processing centre.
“A person staying at our Manston facility has sadly died in hospital this morning after becoming unwell,” the UK Home Office wrote on Twitter on Saturday.
“We express our heartfelt condolences to all those affected.”
The man arrived on November 12 in the UK on a small boat from France and was in the Manston processing centre in Kent, which has been under scrutiny for weeks.
The Home Office said the man was not believed to be suffering any infectious illness but some unconfirmed reports suggest he had contracted sepsis.
The case has been referred to the coroner and the Independent Office for Police Conduct (IOPC).
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We take the safety of those in our care extremely seriously and are profoundly saddened by this event. A post-mortem examination will take place so it would not be appropriate to comment further at this time. (2/2)— Home Office (@ukhomeoffice) November 19, 2022
Conditions at Manston have been widely criticised, as around 4,000 people kept there for processing were forced to share accommodations.
The facility is intended to house around 1,500 migrants for less than 24 hours at a time.
In early November, media reported widely on the "appalling and inhumane" conditions at the centre, including the story of a young girl who threw a bottle to journalists containing a letter asking for help for pregnant women and sick detainees who were at the centre for more than 30 days.
The Home Office transferred hundreds of people out of Manston amid these reports.
British Home Secretary Suella Braverman and her French counterpart signed a deal last week to ramp up efforts to end Channel crossings that have topped 40,000 in 2022.
The rising numbers of asylum seekers have caused a logjam in asylum claims and increased accommodation costs, estimated by the UK government at £6.8 million ($7.8 million) a day, straining local services and fuelling public anger.
But refugee rights groups accuse the government of a callous and chaotic approach, particularly after reports emerged of the unsafe conditions that developed at Manston.
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