Television footage showed the plane crashed upside down in the wreckage of a burnt-out house as firefighters and rescue officials scoured the smoking ruins. Several other houses nearby also appeared to be badly damaged, Reuters reported citing public broadcaster NHK.
NHK said two men inside the small plane, which was carrying five people, were killed. A woman who was inside one of the houses was also killed and five people were injured, it said.
"I heard a tremendous sound like a truck crashed into a house... When I looked outside from a window, fire was flaring up," an unidentified woman told NHK.
"The fire was blazing up so hard," she said.
The Tokyo Fire Department said three people were "in cardiopulmonary arrest", a description usually used by officials in Japan until deaths are confirmed by a medical examiner.
The fire department also said five houses and at least two cars had been set ablaze.