The group, called Army of Ansar al-Sunna, posted a video showing identification papers and a passport bearing the name of Akihiko Saito, 44, a former paratrooper and veteran of the French Foreign Legion, who has been missing in Iraq since 8 May.
The footage, which was not dated but was seen by Reuters on Saturday, showed the body of a dead man lying on his back with blood covering his face. He appeared to resemble Saito's pictures.
"I saw the footage and confirmed that it was my older brother," Hironobu Saito said in a handwritten statement to media organisations, adding that he had conveyed his view to police and to the Japanese Foreign Ministry.
A Foreign Ministry official said, however, that the ministry was still making checks.
"The Foreign Ministry will continue to make efforts for confirmation by also collecting information from Hart Security," the official told Reuters, referring to the British security firm employing Saito.
Six Japanese civilians have been taken hostage since the war in Iraq began.
Backpacker Shosei Koda was beheaded by militants in October, but the others were released unharmed.
The Japanese Foreign Ministry
said it was still making checks
In addition, two Japanese diplomats and two Japanese freelance journalists had been killed in Iraq.
Army of Ansar al-Sunna, one of the main Sunni Muslim insurgent groups, has claimed responsibility for attacks against US forces and the Iraqi government and killed several hostages.
This month, the militant group said it had seriously injured Saito after abducting him in an ambush of a convoy of cars coming from a US base near Baghdad.