A Government spokesperson said the man, who died last Saturday, tested positive for the infection and a coroner would confirm the cause of death in due course.
It is understood the man arrived in the UK as part of a small boat crossing on 12 November and was taken to the Manston processing centre.
He is believed to have been taken ill on the evening of 18 November and was taken to the nearest hospital where he died the following morning.
The Government spokesperson said: “Our thoughts remain with the family of the man who has died and all those affected by this loss.
“Initial test results processed by a local hospital for an infectious disease were negative, but a follow-up PCR test was positive, indicating that diphtheria may be the cause of the illness. The coroner will conclude in due course.
“We take the safety and welfare of those in our care extremely seriously and are taking all of the necessary steps following these results.
“We are offering diphtheria vaccinations to people at Manston, which has 24/7 health facilities and trained medical staff.”
The Government has faced heavy criticism for the conditions within the Manston processing centre, with migrants reporting conditions including overcrowding and scabies.
At one point as many as 4,000 people were being detained at the site, which is designed to hold just 1,600. This number later dropped to within capacity.
Earlier this month the Home Office began vaccinating asylum seekers against diphtheria after dozens of cases were discovered within processing centres across England.
Diphtheria is a contagious, airborne infection and thrives in areas of poor sanitation. It can be fatal but vaccines and antibiotics are highly effective.
Legally, asylum seekers are not meant to be held for more than 24 hours at Manston as the site is a non-residential facility. A Home Office minister said earlier this month that it had been operating outside of this limit while over capacity.