The Free Syria Army, the main rebel fighters in Syria, distanced themselves from Jabhat al-Nusra following the new revelations.
"We don't support the ideology of Al-Nusra," Louay Muqdad, FSA spokesman, told AFP news agency, stressing: "There has never been and there will never be a decision at the command level to coordinate with Al-Nusra."
Al Jazeera's Sue Turton, reporting from Antakya in neighbouring Turkey, said the conflicting statements confirm the divisions between group fighting against the Syrian government.
"The first statement came from the leader of Jabhat al-Nusra, [Abu Muhammed Al-Julani] who gave the first real confirmation that his group was affiliated with al-Qaeda, he even said that the Iraqi al-Qaeda had given the group half of its money to start the fight against the regime," she said.
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"But he insisted that this did not mean it would sideline the other groups they were fighting alongside of against the Assad regime.:
Julani said in the video that his group would not be changing its "behaviour".
"Al-Nusra Front will not change its flag, though we will continue to be proud of the flag of the Islamic State of Iraq, of those who carry it and those who sacrifice themselves and shed their blood for it," Julani said, acknowledging he had fought in Iraq alongside al-Qaeda's Iraqi branch.
"We reassure our brothers in Syria that Al-Nusra Front's behaviour will remain faithful to the image you have come to know, and that our allegiance [to al-Qaeda] will not affect our politics in any way."
Al Jazeera could not independently verify that the audio clip was a genuine recording.
Meanwhile, a Syrian fighter jet dropped five shells on Wednesday on a rural area in northeastern Lebanon near the Syrian border, a military official told AFP news agency.
"A Syrian jet dropped five shells on the outskirts of Sarjal Ajram. No one was hurt," the official said on condition of anonymity.