Princess Cruises says it is surprised and disappointed that the Falkland Islands government turned away its Star Princess ship.
The ship had planned to dock in Port Stanley on a cruise from Chile to Brazil, with stops in Argentina.
Many Argentines are among the 3,500 passengers and crew.
The cruise comes as Argentina and Britain engage in a diplomatic row over the islands Argentina calls the Malvinas.
Falklands government spokesman Darren Christie said they had to deny entry because some passengers had stomach flu and the islands are ill-equipped to handle a contagious virus.
But Princess Cruises said the decision was unwarranted and unscientific and runs against international health policy.
Hundreds died when Britain drove out occupying Argentine forces in 1982.