In a message he read by telephone on Aljazeera from the holy city of al-Qum in Iran, Sadr said: "Shia and Sunni mosques are being attacked as if we were enemies."
"No, we are brothers, we are brothers in Islam and peace. Love each other and do not attack each other. The blood, property and honour of a Muslim is sacrosanct ... the unity of Iraq is your responsibility."
Al-Sadr, who has been on a tour of Iran and Arab countries since late January, warned against "a plan by the occupation to spark a sectarian war," and called on Sunni groups such as the Association of Muslim Scholars to form a joint panel that would prevent sectarian attacks.
He also called on Sunni and Shia leaders to sign a pledge that would "forbid sectarian attacks and condemn extremists".
Earlier an official with Sadr's al-Mahdi Army movement in Najaf, south of Baghdad, said al-Sadr had ordered members of his militia to protect Sunni mosques in majority Shia areas in southern Iraq.
"The blood, property and honour of a Muslim is sacrosanct ... the unity of Iraq is your responsibility"
Muqtada al-Sadr, Iraqi Shia cleric
Saheb al-Amiri said: "Muqtada al-Sadr has ordered the al-Mahdi Army to protect Sunni mosques and religious places in Basra and in other regions" where his movement is influential.
More than 130 people, mostly Sunnis, have been killed and many Sunni mosques ransacked over the past two days in a wave of retaliation attacks after the bombing on Wednesday of the golden-domed Ali al-Hadi mausoleum, one of the countries' main Shia shrines, in Samarra, north of Baghdad.