The five-seater plane crashed at around 11:00 am (0200 GMT) shortly after it departed from Tokyo's Chofu airport, public broadcaster NHK reported.
"Four people were involved in the accident and three of them were rescued, but we don't know about further details, including their condition," a spokesman at the Tokyo Fire Department said, adding that it was also not clear how many people were aboard the plane.
NHK, quoting police, said two people on board and one female local resident were killed in the accident.
"I thought it was flying quite low," a local resident who witnessed the crash told NHK.
Television footage showed firefighters battling the inferno, as well as the remains of the plane's tail.