Police have reportedly described the body parts as having no apparent injuries apart from where they were severed. A woman's torso and "a pair of soil-covered arms" were found in Shimamoto while legs were found in Yamashina.
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.
Investigators told Kyodo news that security footage appeared to show Bayraktar and the missing woman walking toward the apartment on February 16, and an inside camera caught the two entering together.
A large amount of air freshener had been used in the condo and part of the woman's driver's license was found there also, the sources said.
According to authorities, they found a woman's head, though her identity had not been confirmed as of the latest reports available.
The man has reportedly denied all the allegations against him.
Bayraktar was the last person to be seen with the missing woman before she disappeared. However, the woman was not found inside.
Police searching for the woman found what they believe to be her head in a suitcase in the apartment. The Asahi Shimbun reports that another American traveler who booked lodging in the same building because of its low cost "expressed bafflement" upon learning of the severed head.
Video records from security cameras and other devices showed that Bayraktar went in and out of the Higashinari condominium several times carrying a large travel bag on February 18.
Yevgeniy Bayraktar was arrested last week for allegedly holding captive a 27-year-old company employee from Hyogo Prefecture. The police have not officially released the name of the suspect, though it has been widely reported in the Japanese news media.
Hyogo Prefecture police, where the unnamed missing woman is from, declined to answer questions Monday night.