"The fighting between Islamist factions should end," he told reporters during his trial in Amman.
"Abu Bakr al-Baghdadi, leader of the Islamic State of Iraq and the Levant (ISIL), should dissolve his group and work under the Nusra Front," he said, referring to orders given by Al-Qaeda leader Ayman al-Zawahiri.
"The two groups should reconcile and focus on fighting those who fight them."
He also called for an "end to kidnappings... You should not kidnap or kill anyone who does not carry weapons to fight you."
The jihadists were initially welcomed by other rebels, but allegations of brutal abuses against civilians as well as rival opposition fighters sparked a backlash, and even accusations that they were serving the interests of the regime.
In some cases, Al-Nusra, the officially recognised Al-Qaeda franchise in Syria, participated in fighting against ISIL, but its leader recently called for reconciliation.
Abu Qatada's remarks came after Al-Qaeda chief Ayman al-Zawahiri ordered the ISIL to stop meddling in Syria and anointed Al-Nusra to carry the network's banner in the civil war.
During his trial, Abu Qatada complained that the "hearings and procedures were too slow," demanding the court "be committed" to a Jordanian-British agreement that led to his deportation from the United Kingdom last summer.
"I came to Jordan because it is a blessed land and I want to die here. You must be committed to the agreement, which has become a law. Otherwise, I will boycott the hearings," he said.
The trial was adjourned until January 30.
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