The agency said it expected some “probable cases” to be downgraded in the coming days.
Dr Anjan Ghosh, director of public health at Kent County Council, told BBC Politics South East that a total of 20 cases had been confirmed and nine were probable.
Sixteen of the 20 confirmed cases were university students and four were secondary school students, he said.
Juliette Kenny, a sixth form pupil at Queen Elizabeth’s Grammar School in Faversham, was one of the two young people to die from the infection last weekend. The second was an unnamed University of Kent student.
Other schools in the Canterbury area with confirmed or suspected cases are Norton Knatchbull School in Ashford, Simon Langton Grammar School for Boys in Canterbury and the Canterbury Academy.
The UKHSA has written to students at EKC Canterbury College asking them to be alert to the signs and symptoms of the disease.
Close contacts of the person affected are being offered antibiotics, it said.
The college was closed on Sunday but students “can continue to attend college as normal”, the agency said in the letter, seen by the BBC.
Some businesses in the city have told the BBC they have seen a decline in footfall as students “hide in their bedrooms“.