The corpse, clad in a camisole and short pants, was not badly decomposed when discovered on June 27, which local reports said indicated the woman had not been dead for long.
But police were unable to confirm the identity of the body as being that of 34-year-old Yang Mei until today, a police spokesman said.
Yang came to Japan in September 2013 as a trainee, one of the tens of thousands of foreigners - mostly from China, Vietnam and Indonesia - who participate in the government's Industrial Trainee and Technical Internship Program (TTIP).
"She was working at an auto-parts plant in Kyoto but disappeared from her dormitory after being seen in its cafeteria in March 2014," the spokesman said.
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He added that police matched the fingerprints of the body with those of Yang from the immigration bureau.
TTIP is officially described as an internship programme under which people from developing countries can learn skills at Japanese companies.
But it has been criticised by rights activists as a scheme to provide cheap labour for the textile, construction, farming, manufacturing and other industries.