Ahmad Abd al-Ghafur al-Samarrai, a cleric in the influential Association of Muslim Scholars, said during Friday prayers that if President Jalal Talabani wanted to begin a new phase, he first had to release those in prison.
The statement, from the religious group most often associated with the Iraqi militias, has been taken as a sign of willingness to work with the new government.
He urged Talabani not to bend to US pressure, particularly from US Defence Secretary Donald Rumsfeld. The US has opposed freeing prisoners or pardoning fighters.
It is unclear how much say Talabani will have in his largely ceremonial post.
Meanwhile, Prime Minister-designate Ibrahim al-Jafari is putting together a cabinet, but it is not known whether the new government will back pardons.
Al-Samarrai's comments came three days after Rumsfeld made a surprise visit to the country and urged the emerging government to avoid politicising the Iraqi military.
Donald Rumsfeld was on his
second visit in three months
Talabani, after he was sworn in as president this month, appealed to Iraq's resistance groups to work with the newly elected leadership and suggested they could be pardoned, although he said the Iraqi government would continue to fight foreign elements.
"We must find political and peaceful solutions with those duped Iraqis who have been involved in terrorism and pardon them, and invite them to join the democratic process," Talabani said after his inauguration.
"But we must firmly counter and isolate the criminal terrorism that's imported from abroad."
The Sunni voice
Most of the 10,500 detainees are held by the US military, and some lawmakers have said the new president is just expressing his personal opinion.
Still, Talabani and other members of the new government are reaching out to Iraq's Sunnis, who are thought to be the backbone of the resistance.
Many Sunnis boycotted the 30 January elections or stayed at home for fear of attack.
Two weeks ago, al-Samarrai instructed his followers to join the security forces.
There have been growing calls to deal with detained Iraqis. Outgoing interim Prime Minister Iyad Allawi recently sent a message to the US military commander in Iraq, General George Casey, asking him to review the prisoners' cases.
In a political development, the office of Iraq's most influential Shia Muslim cleric, Grand Ayat Allah Ali al-Sistani, said he did not want leading Shia lawmakers to take posts in the cabinet because he wanted them to focus on the National Assembly's main task of writing a constitution.
Iyad Allawi has made a call
for prisoners to be pardoned
Al-Sistani has largely stayed out of politics, but Friday's comment was a sign he may take a greater role. The Shia-led United Iraqi Alliance's 140 seats make it the biggest bloc in the 275-member assembly.