But Saleh Nikbakht denied that he had said the court would quash the ruling.
Suggestions that the death penalty had been overturned led to widespread rioting on Saturday with clerics threatening to carry out the execution themselves.
"I just said that it has been heard that the verdict was overturned," said Mr Nikbakht.
Meanwhile on Saturday, a local head of Iran's main reformist party, the Islamic Iran Participation Front (IIPF), began a six-month jail sentence for voicing support for Professor Aghajari.
The fact that the supreme court based in the holy city of Qom is reviewing Professor Aghajari's case indicates "the death sentence has almost certainly been revoked," say legal experts.
"If politics don't interfere in the case, the verdict can never be upheld by the Supreme Court," Naser Qavami head of the parliament's judicial committee told Associated Press.
'Monkeys'
Professor Aghajari enraged conservatives last summer when he said that Muslims should not uncritically follow the line laid down by Islamic clerics "like monkeys".
He questioned why clerics alone had the right to interpret Islam, which led many to accuse him of being "Iran's Salman Rushdie".
But the sentencing of the academic to death led to student protests.
Professor Aghajari has said that he will not appeal against the death sentence.
According to his lawyer, he believes that "those who have issued this verdict have to implement it if they think it is right or else the judiciary has to handle it".
In addition to the death penalty, he was sentenced to eight years' internal exile in remote areas of Iran and banned from teaching for 10 years.
The human rights group, Amnesty International, has taken up his case.
The organisation says the academic is in need of medical attention because of problems with the remaining part of his right leg.
Professor Aghajari, a 45-year-old war veteran, was disabled during the 1980-88 Iran-Iraq conflict.