The blaze started early Tuesday at a two-story wooden house in the Kopli neighborhood in the Estonian capital, rescue board spokesman Toomas Viks said. The cause of the fire was not immediately clear.
The bodies of three men and three women were found in one large apartment on the second floor, Viks said. Two people escaped the blaze with minor injuries, he added.
Viks said the building was known to be used by homeless people, though he could not say whether the victims were homeless.
"We hope to get details after police have identified the victims," he said.
The building was engulfed in thick black smoke when firefighters arrived at the scene in the middle of the night, and suffered serious damage before the blaze was extinguished.
Estonia has one of the worst fire safety records in Europe, and in the past has topped lists for the number of fire-related deaths per capita.