Ibuki Kizu was found by police at 12.50am on Sunday at her 43-year-old dad’s shop in Tokyo.
Police said she appeared to have marks on her neck which indicated pressure had been applied to it.
Her dad was found hanged from a tree a few hours after his daughter’s body was discovered in Saitama, a city around 15 miles from Tokyo.
Police believe he murdered his daughter before killing himself.
On Saturday afternoon he apparently told a family friend he “stabbed his daughter at the shop” and was going to drown himself in a river, Japan Times reported.
Police made the grim discovery of Miss Kizu’s body after the teenager’s mother had told police that she could not contact her daughter and husband.
The refrigerator is said to be 85 cm high, 140 cm wide and 70 cm deep.
The family lives in a house near the shop.
Th teenager, who lived with her parents and a younger brother, left for work on Saturday morning but failed to arrive.
A woman, 70, who runs a flower shop in the area, said: “The daughter was very gentle and quiet, and the father really loved his kids.”