It quoted Japanese officials as saying the two patients were not outwardly displaying symptoms of the virus but were being treated in Japan.
The vessel had at least 3,700 people on board, South Africa’s authorities said in a statement.
When a passenger, who disembarked in Hong Kong, tested positive for the virus at the end of January, the ship was quarantined for a four-week period, the statement added.
Ten other South African crew members are still on board the Diamond Princess cruise ship, and won’t be allowed to disembark until they pass a two-week quarantine period and test negative for the virus.
Passengers are being prioritised for disembarking before crew, the South African health ministry said quoting the cruise company.