The outbreak was found in soyabeans planted 30 days ago in Primavera do Leste, an important soya area in south-eastern Mato Grosso, Brazil's biggest soya producing state, Embrapa Soya's chief plant pathologist, Jose Yorinori Tadashi, said.
"We are going to the area on Sunday to assess the extent of the outbreak and discuss control measures," Tadashi told Reuters by phone from Londrina.
He said that the Mato Grosso Foundation for Agricultural and Livestock Research (Fundacao MT) had reported the outbreak to Embrapa.
Only about 5 percent of the new soyabean crop has been planted in Primavera do Leste though more has been sown in the center-north part of the state.
Primavera do Leste is vulnerable to soya rust because it harvests soya in summer and winter so there is no crop rotation to break the rust cycle.
In 2003/04, soya rust caused an estimated 4.5 million tonnes loss out of a crop of just over 50 million tonnes. Losses fell in 2004/05 due to drier weather and increased spraying.
Brazil is the world's second-largest soyabean producer and exporter after the United States.