The Japanese police on Monday began investigating the plane crash in a Tokyo suburb on Sunday.
Five men were on board the small Piper PA-46 plane when it ploughed into a house in Chofu city and burst into flames, NHK news agency reported.
The crash killed a 34-year-old woman living in the house, as well as the pilot and another person on the plane. The three other men on the plane and two people on the ground received injuries.
Investigators have said that the plane went down less than a minute after takeoff from nearby Chofu airport.
Witnesses say it looked as though the aircraft never gained sufficient altitude. Police suspect a mechanical problem caused the crash.
The Tokyo metropolitan government, which administers the airport, has requested owners and pilots of small planes to refrain from using the airfield until the cause of the crash is known.