Having strong links with the Syrian government, Russia fears that the international terrorist organisation could turn Syria into its Mideast base.
"Russia strongly and unequivocally condemns terrorism in any of its forms and manifestations," the Russian foreign ministry said in a statement on its website on Thursday.
The group, Al-Nusra Front, also denies an earlier claim that it has merged with Iraq's Al Qaeda affiliate, according to an audio message purported to be from al-Nusra general commander Abu Muhammad al-Joulani.
The message was posted on various radical Islamist websites known for posting similar statements by Al Qaeda figures.
Al-Joulani's message comes after the leader of the al Qaeda-affiliated Islamic State of Iraq purportedly claimed this week in an audio statement that Al-Nusra Front is part of its network.
A speaker identifying himself as Islamic State of Iraq leader Abu Bakr al-Baghdadi had said -- in a message posted to online jihadist forums -- that the two groups would combine their names and be known as "The Islamic State of Iraq and the Levant (Syria)."
But Al-Joulani distanced himself from al-Baghdadi's message, saying it took Al-Nusra off guard.
"We would like to inform the public that we were not informed or consulted of the content of the announcement," al-Joulani said.
Despite denying a merger, Al-Joulani said that he is raising the bar higher by pledging allegiance to al Qaeda leader Ayman al-Zawahiri.
Al-Joulani's message comes a week after the White House, according to US officials, signed off on new nonlethal aid for Syrian rebels. Officials said it is expected to include equipment such as body armor, night vision goggles and other military equipment that is defensive in nature, but could be used to aid in combat by Syrian rebels battling forces loyal to President Bashar al-Assad.
Meanwhile, Syria's Foreign Ministry has complained to the UN about al Qaeda activities in the country.
Syria's Foreign Ministry complained to the United Nations and the UN Security Council on Thursday about al Qaeda's activities in the country.
In a letter to the United Nations, the ministry said it "expects the Security Council to fulfil its role and preserve global security," and classify the Al-Nusra Front as an al Qaeda-linked group, state media reported.
UN sanctions are are already in place to punish individuals and entities linked to al Qaeda, by freezing assets, banning travel and imposing an embargo on arms destined for the terror network.
The rebel group's pledge of allegiance has also deepened Western concerns that weapons could fall into the wrong hands.
The US and EU are currently providing non-lethal aid and are beginning to distribute food and medical supplies to the Free Syrian Army, however, they have stopped short of providing arms.
The opposition renewed their appeals for arms on Wednesday on the sidelines of a meeting with the Group of Eight (G8) in London. The outgunned opposition have called for the arms in order to fight Assad's regime in a conflict that is now in its third year and has cost some 70,000 lives, according to the UN.