Al-Qaeda’s top leader has ruled against the merger of two jihadi groups based in Syria and Iraq, in an attempt to put an end to increased tensions and infighting among members.

Ayman al-Zawahiri’s ruling came in a letter addressed to the leaders of Syrian-based Jabhat al-Nusra and the Islamic State in Iraq (ISI), which is the largest jihadi umbrella group in the country.

Al Jazeera exclusively obtained a copy of the letter on Sunday from reliable sources in Syria (translated here).

The ruling comes two months after the leader of ISI, Abu Bakr al-Baghdadi, declared a merger with al-Nusra to form the Islamic State of Iraq and the Levant (ISIL), saying that al-Nusra was "merely an extension and part of the Islamic State of Iraq".

Al Jazeera received an original copy of Zawahiri's letter to the warring Jihadi groups

However, the unilateral move led to defections, infighting and a breakdown in operations as members disagreed over who commanded the battlefield.

In the letter, Zawahiri said Baghdadi was "wrong" to declare the merger without consulting or even alerting al-Qaeda's leadership. He added that Syria was the "spatial state" for al-Nusra, headed by Abou Mohammad al-Joulani, while Baghdadi’s rule would be limited to Iraq.

Al-Nusra, listed as a terrorist organisation by the US for its affiliation with al-Qaeda, is considered to be one of the most effective rebel groups in Syria.

But after Baghdadi released a video in April declaring the formation of the ISIL, many of al-Nusra’s fighters, especially non-Syrians, left to join the new umbrella group.

"This was the most dangerous development in the history of global jihad," an al-Nusra source inside Syria told Al Jazeera on Saturday.

One al-Nusra fighter estimated that 70 percent of the group's members left for the ISIL in Idlib province, with even higher defection rates in the Syria’s eastern regions.

Aleppo, the bastion of al-Nusra, saw the least defections from its ranks, fighters said. But even then the city suffered from the divisions within the group.

The division made the everyday practices of governance and fighting even more challenging.

Last week, activists reported flour shortage in the northern city because fighters protecting the silos had expressed their allegiance to ISIL and did not recognise the legal committee - headed by Nusra and other Syrian batalions - responsible for distributing flour. Several parties had to intervene to end the crisis.

Iraq-Syria cooperation

The divisions and turf battles between commanders prompted both Joulani and Baghdadi to send separate letters to Zawahiri in Afghanistan to arbitrate between the two groups.

"The proponents of Jihad were all dismayed by the dispute that occurred on the media between our beloved brothers in the Islamic state of Iraq and Jabhat al-Nusra," Zawahiri said in the letter.

However, he called on both sides to cooperate and, whenever they could, support each other with money, weaponry and fighters.

Zawahiri also called on members of both outfits to refrain from infighting and named Abou Khaled al-Soury, local Syrian commander, as a personal emissary "to oversee the implementation" of the accord.

When Baghdadi released the merger statement two months ago, Joulani issued an audio recording saying he had not been consulted on the formation of the ISIL and insisted his fighters would continue to operate under the al-Nusra banner.

But that message did not deter Baghdadi from travelling from Iraq to the suburbs of Aleppo and trying to open offices there.

It is unclear whether Baghdadi will accept the al-Qaeda leader’s ruling, and what effect it will have on the ground.

The fighters who left al-Nusra to join the ISIL might not want to rejoin the group, according to those close to Baghdadi.

"Ninety percent of the Arab and foreign fighters [battling in Syria] joined ISIL," said Abu Osama al-Iraqi, an activist affiliated with the Islamic State of Iraq.

"It will be hard for them to take a step backward."

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