A ministry official said studies were underway into the efficacy of vaccines against the new variant, which differs from highly infectious variants first found in Britain and South Africa that have driven a surge in cases.
"At the moment, there is no proof showing the new variant found in those from Brazil is high in infectiousness," Takaji Wakita, head of the National Institute of Infectious Diseases, told a health ministry briefing.
Still, Brazil's Health Ministry said it has been notified by Japan's authorities that the new variant has 12 mutations, and one of them has already been identified also in the variants found in the United Kingdom and in South Africa.
"It implies in a potential higher virus infectiousness," it said.
Of the four travellers who arrived at Tokyo's Haneda Airport on 2 January, a man in his forties had a problem breathing, a woman in her thirties had a headache and sore throat and a man in his teens had a fever, while a woman in her teens showed no symptoms, the health ministry said.
All travellers were in quarantine at the airport, Brazil's Health Ministry said.
After seeing a steep rise in coronavirus cases, Japan declared a state of emergency for Tokyo and three prefectures neighbouring the capital on Thursday.
Nationwide cases have totalled about 289,000, with 4061 deaths, public broadcaster NHK said.