The body has been identified as Shosei Koda. From The Scotsman, with thanks to Kemaste:
The Japanese government confirmed today that a decapitated body found in Iraq is that of a Japanese man taken hostage by Islamic militants earlier this week.
The body found in central Baghdad yesterday has been identified as Shosei Koda, 24, Foreign Minister Nobutaka Machimura told reporters at an emergency news conference.
Japanese Embassy officials in Baghdad had sent fingerprints of the body to the Foreign Ministry in Tokyo, and police experts had positively identified the body, Machimura said.
Islamic guerrillas had threatened on Tuesday to behead Koda within 48 hours unless Japan pulled its troops out of Iraq. Tokyo immediately refused, and the deadline passed with no word of Koda’s fate. The group has not yet made a claim of responsibility.
Iraqi officials found Koda’s decapitated body in Baghdad on Saturday. Associated Press Television News videotape showed the severed head with the hostage’s long black hair and features.