The message again demanded the release of Sajida al-Rishawi, an Iraqi woman sentenced to death in Jordan for involvement in a 2005 terror attack that killed 60 people.
It also mentioned for the first time Jordanian pilot 1st Lt. Mu'ath al-Kaseasbeh, who is a captive of the Islamic State group, setting tomorrow afternoon deadline.
Today's video matched a message released over the weekend, though neither bore the logo of the Islamic State group's al-Furqan media arm. The weekend video showed a still photo of Kenji Goto holding what appears to be a photo of the body of Japanese hostage Haruna Yukawa.
The message says that unless the Jordanian government frees al-Rishawi within 24 hours, Goto and the pilot will be killed, adding that this would be the group's last message. The message warns any delaying tactics by the government will result in the death of both men.
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Japanese officials held emergency meetings after the video's release.
"In this extremely tough situation, we are continuing as before to request the cooperation of the Jordanian government to work toward the immediate release of Mr. Goto," Suga said.
A Japanese envoy in Jordan, Deputy Foreign Minister Yasuhide Nakayama, earlier expressed hope the two hostages would return home "with a smile on their faces.