Al-Zawahiri also stressed that the militant group of Al-Nusra Front was the branch of the al-Qaeda in Syria.
"The Islamic State in Iraq and the Levant (ISIL) is to be abolished, while the Islamic State of Iraq (ISI) remains functioning," he said.
Zawahiri said the leader of Al-Qaeda in Iraq, Abu Bakr al-Baghdadi, "has made a mistake by establishing the Islamic state of Iraq and the Levant without asking for our permission, or even informing us."
It was not immediately clear when he made the remarks.
Meanwhile, Zawahiri added that the leader of the Al-Nusra Front in Syria, Abu Mohammad al-Jawlani, "has made a mistake by announcing his rejection of the ISIL, without taking our permission, or even informing us."
He said the rule of ISI will be confined to Iraq, while the Al-Nusra Front in Syria will be "an independent branch of Al-Qaeda that reports to the general command."
The militant group of ISIL is mainly blamed for an escalating abuse against Syrian civilians, including kidnappings and public executions in areas under the control of foreign backed militant groups.
Divisions are deepening among foreign-backed militant groups in Syria.
Tolerating consecutive defeats imposed by Syrian army to the al-Qaeda linked group of the Islamic State in Iraq and the Levant within recent days, is seemed to be main reason over disbanding such group.
Plots by the US and its allies to destroy Syria through supporting militancy in the Arab country have also failed as the foreign-backed terrorists are now self-destructing.
Over the past months, rivalries and infighting have been on the rise among the highly-divided militants operating inside Syria.
Foreign-sponsored militancy in Syria has taken its toll on the lives of many people, including large numbers of Syrian soldiers and security personnel, since March 2011.
NJF/NJF