Health regulator Anvisa was alerted on Monday to the possible infection in a patient admitted to an adult intensive care unit in a hospital in the northeastern state of Bahia, according to a ministry statement.
Candida auris, which the health ministry said poses "a serious threat to global health", was first identified in Japan in 2009.
It can spread particularly quickly in healthcare environments and between hospital patients.
A health task force has been set up to study this case more closely and prevent the fungus from spreading, the ministry said.
The first Candida auris case in Britain was in 2013 and in the United States in 2016. It has been identified in dozens of countries, being more prevalent in South America and South Asia.
Brazil's public health system has been under huge pressure this year due to the Covid-19 pandemic.
The country has the second highest death toll in the world at 177,317, and the third highest number of confirmed cases at 6.62 million.
