Japan believes that latest message, which was originally uploaded on YouTube, featuring Mr Goto is genuine.
Japan's chief cabinet secretary Yoshihide Suga said: "We are still in the process of verification but with all of the information gathered we think that there is a high probability that the voice was indeed that of Mr Goto."
In it the 49-year-old father of two can be heard saying: "I'm Kenji Goto Jogo. This is a voice message I've been told to send to you. If Sajida al-Rishawi is not ready for exchange for my life on the Turkish border by Thursday sunset 29th of January Mosul time, the Jordanian pilot Muath al Kasaesbeh will be killed immediately."
Jordan has already said it is willing to hand over Iraqi would-be-suicide bomber Sajida al-Rishawi once it knows Jordanian pilot Moaz al-Kasasbeh is safe and will be released, but it remains unclear if Christian Japanese journalist Kenji Goto will be included in any potential deal.
Nations around the world, including the US believe the deal with IS should not go ahead.
Christian Middle East analyst Simon Barrett believes such an exchange could set a dangerous precedent, encouraging terrorists to take more people hostage. Speaking on Premier's 'News Hour', he said: We got to be very careful, certainly Western governments do that we don't actually play into the hands of ISIS (Islamic State) and give them a huge PR coup that could encourage the releasing of more Islamic State or al-Qaeda terrorist from Western jails."
Simon Barrett speaking to Marcus Jones on Premier's 'News Hour':