Iraqis must "unite to fight terrorism and to get rid of people like al-Qaida," said the cleric Hazem al-Araji.
These groups "sometimes act in the name of Ansar as-Sunna (partisans of the Sunnis), but they are enemies of the Sunnis," he said on Thursday.
"You who call yourselves Qaida al-Jihad (base of the holy war), you are the base of apostasy," he said, referring to Abu Musab al-Zarqawi's group.
Threat to kill
Al-Qaida in Iraq is a shadowy group allegedly headed by Jordanian Abu Musab al-Zarqawi and is blamed for bloody attacks that have often targeted civilians.
Since Saturday, at least 71 people have been killed in bombing attacks on Shia Muslim targets.
The comments came as the Moroccan government condemned as "extreme barbarity" an apparent announcement by the group that it planned to kill two kidnapped Moroccan embassy employees.
Iraqis are celebrating the
Muslim festival of Eid al-Fitr
The claim came in an internet statement attributed to Al-Qaida in Iraq.
"After examining the cases of the detainees, the court decided that they were without doubt loyalists of the oppressors and elements of the apostate regime in Morocco," said the statement.
"Based on that, the Sharia [Islamic law] court of the al-Qaida Organisation in the Land of Two Rivers [Iraq] has decided to apply God's judgment on apostates and ruled that they be executed."
Embassy driver Abd al-Rahim Boualam and agent Abd al-Karim al-Mouhafidi went missing on 20 October while travelling on the treacherous highway between Amman and the Iraqi capital Baghdad.
The Moroccan government said the act was "totally against the noble precepts of Islam" and the "fundamental values of humanity".
"I beg our mujahidin brothers in Iraq, who are Muslims by the Islamic law and justice they live by, to release my husband and his friend. They haven't done anything"
Liqaa Abbas Mirza,
Wife of Moroccan hostage
The alleged al-Qaida announcement came after relatives of the hostages appeared on Aljazeera to appeal for the lives of their loved ones.
"I beg our mujahidin brothers in Iraq, who are Muslims by the Islamic law and justice they live by, to release my husband and his friend. They haven't done anything. I am Iraqi," al-Mouhafidi's blind and pregnant wife Liqaa Abbas Mirza told Aljazeera by telephone from Baghdad before breaking off in tears.
In a separate statement, al-Qaida also claimed responsibility for Wednesday's downing of a US attack helicopter in western Iraq that killed two marines.
The claim followed comments from US army General Rick Lynch that the AH-1 Super Cobra might have been downed by a missile fired from the ground.
Al-Qaida in Iraq said it shot
down a US military helicopter
"People on the ground believe they saw a munition fired at the helicopter," he said. They "saw the helicopter break into pieces in mid-air and then crash."
US forces then "found in that general area ... a command and control bunker for enemy insurgents," Lynch said. An F-18 fighter jet was called in to bomb the bunker.
Elsewhere in Iraq a US military policeman was killed on Thursday near Baquba, north of Baghdad, the military said, bringing to eight the number of US personnel killed over the past three days.
In the south of the capital, Baghdad, the authorities discovered 11 bodies decomposing at a water purification station, six of which had been decapitated.
Two members of the Iraq government's Wolf Brigades were killed in a gun battle in Dura, south of Baghdad.
In Britain, charges against seven British soldiers accused of murdering an Iraqi teenager in May 2003 were dropped after the judge ruled there was insufficient evidence.