The child is now under isolation at a local hospital, said Nyamdorj Tsogbadrakh, director of the NCZD on Friday.
The child showed symptoms of high-grade fever and skin rashes after playing with a dead marmot, the official added.
A total of seven suspected cases of bubonic plague have been reported across the country so far this year, three of which had been confirmed by laboratory test results.
Two cases of bubonic plague have been confirmed in Tsetseg soum in Khovd Province earlier this month.
A 15-year-old boy in Govi-Altai province died from bubonic plague last week.
Up to 17 out of all 21 provinces in Mongolia are now at risk for the bubonic plague, according to the NCZD.
Health Minister Togtmol Munkhsaikhan has ordered all relevant officials to ensure that health organizations are ready, including training health workers in high-risk provinces and raising public awareness about the infectious disease.
Bubonic plague is a bacterial disease spread by fleas living on wild rodents such as marmots. It can kill an adult in less than 24 hours if not treated in time, according to the World Health Organization.