Failures at the Manston processing centre in Kent led to asylum seekers being sent around the country with diphtheria.
The site was cleared last week with all migrants moved into hotels, but Channel crossings resumed on Monday as bad weather cleared.
Some public health experts raised concerns about the spread of the disease as migrants were moved to hotels.
A man held at Manston died in hospital after crossing the Channel seven days earlier. Gareth Fuller
The infection affects the nose, throat and sometimes skin. It can be fatal if not treated quickly but the NHS says it is rare in the UK and can be treated with antibiotics and other medicines.
A man held at Manston died in hospital on November 19 after crossing the Channel seven days earlier, Government officials said.
Although initial tests came back negative, a follow-up PCR test indicated “diphtheria may be the cause of the illness”.
By November 10, the UK Health Security Agency (UKHSA) had identified 39 diphtheria cases among asylum seekers in England this year.
The number is understood to have risen to about 50, with officials expected to confirm the figure later.
Health officials believe the timings of testing and the onset of symptoms indicate all cases were caught abroad, but they have not been able to rule out transmission in migrant centres.
Downing Street said the Government is “working with local councils”. Gareth Fuller
Dozens of asylum seekers who had contracted the disease were infected before they arrived in the UK, Transport Secretary Mark Harper said on Sunday.
Health Secretary Steve Barclay, during a visit to the Royal Marsden Hospital in London, said: “We vaccinated a range of people at Manston before they were moved, so that was part of the targeted action that UKHSA put in place.
“Clearly within the population as a whole it’s very low risk, because there’s very high uptake of vaccinations within the local population, but we’re monitoring it closely and that’s why so many people were vaccinated – 500 were vaccinated before they left Manston.”
Asked if councils taking in migrants from Manston have been warned about the risks of the highly contagious disease, Downing Street said the Government is “working with local councils”.
The Prime Minister’s official spokesman told reporters: “We take the safety and welfare of people accommodated at these sites very seriously.
“We’re working closely with the UK Health Security Agency and other health professionals and indeed councils to make sure all medical guidance and the robust protocols are followed and that we have contingency plans.”