Authorities found a torso and two arms in the mountains near the western city of Osaka and two legs in Japan's ancient capital of Kyoto, some 50km away, according to local media.
In a separate case on Japan's northern island of Hokkaido, three men have been arrested over suspicions they abandoned the body of a woman missing since December.
The woman met the suspect near JR Morinomiya Station in Osaka around midnight, and security camera footage showed them entering the Higashinari lodging together.
The torso and two arms were uncovered in Shimamoto, and the legs were found in Yamashina.
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"I never heard of a trouble here, so I'm surprised", a 73-year-old resident of the same building the severed head was found said.
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They believe that all belong to the same woman, described as a 27-year-old company employee from Sanda, in Hyogo prefecture, 25 miles from Osaka.
Though she was not seen on video again, the man was spotted entering and leaving the apartment multiple times by himself while carrying a large bag.
During his stay for about a week from February 12 at the Higashinari lodging, security camera footage showed four or five women entering the premises with a man believed to be the suspect, the sources said.
The Washington Post said the woman had told friends she was "going to see an American for a date" and told Instagram followers in a February 15 posting she was off to "meet Jay". She was reported missing when she was unable to be contacted or located after her mobile phone died.
He had taken several other women to the same condominium, but the police have already confirmed the safety of all of them. A new warrant is to be served to the American man for disposing of and damaging a body.