Police believe the head, which was found in a suitcase, belongs to a Japanese woman who was last seen on CCTV footage walking with the suspect.
The woman, 27, had apparently told friends she was going to see an American she had met on an app.
The suspect has allegedly denied any connection with the case.
He has been identified in local media as Yevgeniy Vasilievich Bayraktar, a 26-year-old from New York.
The woman is believed to have visited another apartment in the western Osaka prefecture with the suspect earlier in February, Japanese broadcaster NHK says.
Police say he was seen carrying a large bag out of the building where he was staying.
No other human remains have been found. (Courtesy BBC)