"After samples were taken and testing, the results came back positive for Lassa fever, which is similar to the Ebola virus but not as virulent," public health minister Dorothee Akoko Kinde-Gazard said.
The two people were among five health workers who died at a hospital in Tanguieta, in the north of the tiny West African nation which borders Nigeria to the west.
"There were five deaths at the hospital in Tanguieta but from the samples taken only two were positive (for Lassa fever)," she told AFP.
The WHO's representative in the country, Youssouf Gamatie, was quoted as saying in the Benin media: "It's lucky that we have detected it in the initial phase."
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Benin's authorities said they were expecting additional medication to deal with any further cases.
According to the WHO, Lassa fever is an acute haemorrhagic illness which belongs to the arenarvirus family of viruses, which also includes the Ebola-like Marburg virus.
It was first identified in 1969 in the north Nigerian town of the same name.
The virus, which is endemic in rodents in west Africa, is transmitted to humans by contact with food or household items contaminated with the animals' faeces and urine.
People with Lassa fever do not display symptoms in 80 per cent of cases but it can cause serious symptoms and death in the remainder.
The US Centres for Disease Control and Prevention said that the number of Lassa fever infections in west Africa every year is between 1,00,000 to 3,00,000, with about 5,000 deaths.