"Sayyed Muqtada was wounded in American bombing," his spokesman Ahmad al-Shinabi said on Friday.
Al-Sadr's assistant Aws al-Khafaji told Aljazeera the Shia leader suffered three injuries to his body but these were not life-threatening.
However, Reuters quoting Iraq's Interior Minister Falah al-Naqib said al-Sadr was unhurt and negotiating with the government to leave the Imam Ali shrine.
"Sayyed Muqtada will not be touched if he leaves the shrine peacefully. A truce has been in force since last night," Naqib told Reuters.
An Iraqi political source said a delegation of tribal leaders and political parties met Prime Minister Iyad Allawi on Thursday and demanded he try to put an end to the US offensive on Najaf, Reuters said.
US troops launched a major
assault on Najaf on Thursday
Al-Sadr's spokesman said he was hurt early on Friday as US-led occupation troops clashed with his fighter near an ancient cemetery in the centre of Najaf.
Another spokesman said al-Sadr had wounds to his arm and chest and was being treated at the sacred Imam Ali mosque, where many of his Al-Mahdi Army fighters have taken refuge.
His wounds were not life-threatening, that spokesman said.
Interior Ministry spokesman Col. Adnan Abd al-Rahman said he had received reports al-Sadr was injured in his chest and leg, but could provide no further details.
Spokesmen quoted al-Sadr as telling his followers after he was wounded, "Act wisely, don't surrender to emotions."
Al-Sadr called on his supporters to continue their "jihad" even if he dies a martyr, shortly after being wounded, reports said quoting a spokesman.
Al-Sadr said talks to defuse a standoff between his Al-Mahdi Army and a joint Iraq-US force have reached no deal but will continue, the reports added.
Another aide, Abd al-Hadi al-Darraji, called on Iraqis to begin a sit-in on Friday near the Green Zone in Baghdad, the location of most Iraqi government ministries, as well as the US and British embassies, to protest against the fighting in Najaf.
"Act wisely, don't surrender to emotions"
Shia leader Muqtada al-Sadr
US occupation forces stormed al-Sadr's home on Thursday during a massive attack against his Al-Mahdi Army in Najaf, but the cleric was not there. US marines also captured the city centre but kept out of a holy shrine.
Al-Sadr is said to be in Najaf's sacred compound housing the Imam Ali shrine, surrounded by his followers.
He has led an uprising against occupation troops for more than a week in the city, vowing to fight "until the last drop of my blood has been spilled".
Al-Sadr's fighters have battled occupation forces since 5 August in a resurgence of a spring uprising that was dormant for two months following a series of truces.