An unnamed female fencer in the team had tested positive on Wednesday, three days after returning home from an epee competition in Hungary.
Two more national team members tested positive on Thursday, while another fencer was given the all-clear.
"We're deeply worried that there would be more confirmed cases from the national team," Yonhap quoted an official from South Korea's fencing federation as saying.
The federation said was awaiting the test results of 26 athletes and coaches currently in self-isolation.
Globally, more than 218,000 people have been infected by the flu-like virus and more than 8,900 have died, including 91 in South Korea, according to a Reuters tally.