The officials said he was injured in a U.S. airstrike last week and then died subsequently, though they wouldn't say how they know he is dead.
But ISIS' media wing, the Aamaq agency, posted a statement online Tuesday saying that a source denied that Shishani had been killed. "The source also confirms the he has not been hurt," the agency said.
The initial U.S. assessment was that he was "likely killed"
in the strike, but further assessments led them to understand he had been injured and only later died, according to U.S. officials.
He was killed along with 12 additional ISIS fighters in a wave of strikes by drones and manned aircraft.
Since then, CNN has learned that Shishani was at a "shura," or meeting with other officials, at the time of the strike. U.S. officials had emphasized at the time it was publicly announced that they were not certain of his death and were assessing whether the strike killed him.
One reason the U.S. initially thought Shishani had been killed is that intercepts of his communications had gone silent, CNN learned.
But this situation was a bit unusual, coming together quicker than most. The strike was quickly called in, one official said, when there was sudden intelligence that Shishani was at the meeting. The aircraft and drones had already been patrolling in the skies.
U.S. officials said Shishani had traveled to the al-Shaddadi area from ISIS' unofficial capital of Raqqa to meet with troops in the region who had been in heavy combat and suffered losses.
The Pentagon has offered different locations for precisely where the strike happened, in one instance saying it was near al-Shaddadi but in a press release indicating it happened near al-Hawl several miles away.
Shishani has had a reputation as one of ISIS' most capable commanders. There has been a $5 million reward on his head from the U.S. State Department. Also known as Omar "the Chechen" al-Shishani, he was born Tarkhan Tayumurazovich Batirashvili and once served in an elite Georgian military unit.
"Batirashvili is a battle-tested leader with experience who had led ISIL fighters in numerous engagements in Iraq and Syria," Pentagon Press Secretary Peter Cook, using a different term for ISIS, said in the statement after the initial strike but before his death was confirmed.
"His potential removal from the battlefield would negatively impact ISIL's ability to recruit foreign fighters -- especially those from Chechnya and the Caucus regions -- and degrade ISIL's ability to coordinate attacks and defense of its strongholds like Raqqah, Syria, and Mosul, Iraq," Cook said.
Shishani joined ISIS in 2013, a U.S. official said, and later was in charge of a prison near Raqqa where the terror organization might have held foreign hostages.
Shishani instructed the group to transport vehicles and weapons to Syria from Iraq in June 2014, and he was eventually named ISIS' northern commander by leader Abu Bakr al-Baghdadi, overseeing military operations in northern Syria, the defense official said.