The group has purportedly threatened to kill the pilot, Lt. Muath al-Kaseasbeh, by sunset unless Jordan frees an Iraqi woman from death row and delivers her to the Turkish border.
The woman, Sajida al-Rishawi, was involved in deadly Amman hotel bombings a decade ago.
Jordanian government spokesman Mohammed al-Momani said on Thursday afternoon that al-Rishawi was still in Jordan, raising doubts that the sunset deadline, which will pass in less than an hour, can be met.
He said: "we want to see a proof of life of the Jordanian pilot and then we can talk about the exchange."
In an earlier audio recording, a voice identifying itself as Japanese freelance journalist Kenji Goto said ISIL would kill fellow hostage al-Kasasbeh if al-Rishawi was not handed over by the end of the day.
"If Sajida al-Rishawi is not ready for exchange for my life at the Turkish border by Thursday sunset, 29th of January, Mosul time, the Jordanian pilot Moaz al-Kasasbeh will be killed immediately," Goto said, in an unverified audio message distributed by ISIL-linked Twitter accounts.
It was not clear from the message, reported by monitoring group SITE Intelligence, if either Goto or Kasasbeh would be freed.
Japanese Prime Minister Shinzo Abe told parliament: "We are aware of the new message ... [and] are verifying [its authenticity]." Japan plays no military part in the fight against ISIL.
The apparent communication breaks an anxious silence from the group since their previous 24-hour deadline for Rishawi expired, around 14:00 GMT Wednesday.
Amman had offered to free the Iraqi woman, who was convicted for her part in the 2005 triple-hotel bombings in the Jordanian capital that killed 60 people, if ISIL released their airman.
"Jordan is ready to release the prisoner Sajida al-Rishawi if the Jordanian pilot is freed unharmed," state television quoted a government spokesman as saying on Wednesday.
"From the start, the position of Jordan was to ensure the safety of our son, the pilot Moaz al-Kasasbeh," it added. The government spokesman made no mention of Japanese hostage Goto.
Jordanian Foreign Minister Nasser Judeh wrote on Twitter shortly before 15:00 GMT that his country was still awaiting confirmation that the pilot was safe.
Al Jazeera's Andrew Simmons, reporting from Amman said: "We are finding another suggestion from the Jordanian government here which was that al-Rishawi was still in jail and if she is going to go all that way for exchange in one day that is hard to work out according to them."
Wednesday passed in a maelstrom of conflicting reports on the fate of the three key players, complicated by linguistic and cultural misunderstandings, and by the high stakes on all sides.
'Save my son'
The atmosphere was tense in Jordan, where the country's involvement in the US-led air raids against ISIL positions is contentious.
"It has caused real difficulties in this country because what was a supportive atmosphere towards the allies against ISIL is now turning against the government," Simmons said.
"ISIL are standing to make possibly more capital in the propaganda stakes out of all of this, realising now that hostages it has have more value alive than dead."
The downing on December 24 of Kasasbeh's F-16 fighter jet over northern Syria and his subsequent capture and humiliation by ISIL exacerbated the situation.
This week the pilot's father begged the government to save his son "at any price".
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