Moaz al-Khatib, head of the National Coalition for Syrian Revolutionary and Opposition Forces, called on JAN to sever its relationship with al-Qaeda, according to various media reports.
In a speech earlier this week before opponents of the Bashar Assad regime in Turkey, al-Khatib called on Syrian Jihadists, specifically JAN, to sever their ties with al-Qaeda and its leadership, to change their name and to clearly associate themselves with the leadership of the Syrian revolution.
Meanwhile, the Free Syrian Army (FSA) distanced itself from JAN, while other opposition battalions affiliated with the FSA, including the Syrian Islamic Liberation Front, condemned and rejected the group's pledge of allegiance to al-Zawahiri, calling instead for unity and moderation.
The Syrian Islamic Liberation Front comprises several Islamist factions, including the Tawhid Brigade, the Farouq Brigade, Liwaa al-Islam and Suqoor al-Sham Brigade.
The Front expressed surprise at al-Qaeda in Iraq's (AQI) statement announcing the establishment of a unified organisation, the Islamic State in Iraq and the Levant.
“We express our surprise over this narrow, partisan approach by people [...] who do not comprehend our reality and the interests of the blessed revolution,” the group said in a statement. “They impose a state on us without consulting us, led by an emir we did not choose or even hear of except through media outlets.”
"Pledging allegiance to someone who does not understand our reality does not serve our people or nation," the group said.
For Omar al-Raqqawi, a field activist in al-Raqa in north-central Syria and member of the Syrian Nonviolence Movement, the relationship between the Syrian opposition and JAN was strained even before JAN pledged allegiance to al-Zawahiri.
Now, things are "clear and out in the open, inside and outside [Syria]", he added.
JAN's pledge of allegiance to al-Zawahiri "exposes JAN's real plan, which is to establish an Islamic state and apply sharia socially and politically", he said.
"This not something that can be imposed by force but must rather be decided by the Syrian people through the ballot box," al-Raqqawi said.
"JAN's recent moves on the ground and [attempts] to undercut some armed factions in their areas were without question a prelude to this announcement," he added.
Al-Raqqawi, interviewed in Egypt, recounts how JAN imposed its control over al-Raqa, leading to clashes between the organisation and area residents.
"They took advantage of our weakness and our need for equipment, weapons, medicine and foodstuffs and bargained with us and everyone else and got us to side with them in exchange for protection," he told Al-Shorfa.
"JAN does not have a large number of fighters from al-Raqa itself, and the majority are jihadists who came from other areas like Homs, the Aleppo countryside and Idlib, as well as Arab jihadists," he said.
"The people of al-Raqa maintained their call for a non-violent movement for a large portion of the revolution," he said. "But when the situation began to escalate and when it became apparent the departure of the regime's army from the area was approaching, it was necessary to secure protection, not only for citizens and their homes but also for vital public facilities such as the museum and the municipality building."
He said town residents agreed that JAN would provide security only at the entrances to al-Raqa to control entries and exits and to stop abuses and violations, he said.
"However, after al-Raqa was liberated [last month], residents were surprised to see JAN elements had spread throughout the city and posted their slogans everywhere," he said. "They gradually imposed their control on bakeries, gas stations and other aspects of daily life."
The people of al-Raqa are now blocking JAN's attempts to impose their authority, such as banning the sale of cigarettes and prohibiting non-veiled women from walking in the street, according to al-Raqqawi.
JAN is also appointing new mosque preachers on the grounds that "none of the former preachers can be trusted", he said.
"This provoked city residents, who began to clash with JAN elements, specifically because JAN banned raising the flag of the Syrian revolution on the grounds it is the flag of non-believers," he said. "The big confrontation occurred in the last week of March, when city residents held a demonstration that included men and women in protest over JAN's authoritarianism."
JAN responded by "declaring al-Raqa the launching point of the Islamic emirate, doing so in front of the provincial headquarters, which led to a confrontation and many arrests by JAN", al-Raqqawi said.
JAN elements in al-Raqa always wear black face covers and dress mostly in black, he said. They raise al-Qaeda's flag and other black flags inscribed with Islamic slogans.
Al-Raqqawi described the current situation in al-Raqa as "very tense".
Tal Abyad is an important border city with a crossing linking al-Raqa province with Turkey.
Halim Moatez, a retired professor and province resident, said JAN emerged in the area after the liberation of Tal Abyad and its border crossing by the FSA last September.
"The first problem arose on account of JAN's flag and the insistence of its elements to raise it at the border crossing," he told Al-Shorfa. "FSA soldiers at the time, however, were able to persuade them to remove it and raise the flag of the Syrian revolution instead."
At the beginning of this month, Moatez said, "JAN elements clashed with al-Farouq Brigade under the command of Abu Azzam, which is in charge of the affairs and security of the crossing. The clash left four people dead and many wounded."
According to Moatez, JAN seeks to take control of the crossing "to hold the reins in the region and expand its control."
Not far from al-Raqa, in the Aleppo province town of Manbij, "the situation is akin to fire under ash due to restrictions enforced by forces loyal to JAN under the guise of a 'sharia committee'," said Mahmoud Rafih, a member of Manbij's co-ordination committee.
"Clashes regularly erupt between FSA soldiers and JAN elements who claim to pursue thieves, bandits and smugglers," Rafih told Al-Shorfa.
He said the situation on the ground reflects JAN's inclination to control the region and exclude all other armed factions from it.
Its elements "are concentrated in liberated areas and they no longer have a heavy presence in combat zones, participating only by way of suicide attacks against military structures and fixed check points", Rafih said.