AU Commission leader Jean Ping said the action could result in problems similar to those in war-torn Somalia, the BBC reported Thursday.
France confirmed it dropped arms to tribal fighters in the mountains southwest of Tripoli, Libya's capital.
Ping, speaking from Equatorial Guinea where leaders met Thursday for an African Union summit said he sees "several problems" with the airdrop.
"The risk of civil war, risk of partition of the country, the risk of Somalia-zation of the country, risk of having arms everywhere ... with terrorism," Ping told the BBC. "These risks will concern the neighboring countries."
Ping said an AU-developed peace plan for Libya presented in March remained valid. The plan calls for a cease-fire so political talks could occur.
News of the weapons delivery to rebels fighting to oust longtime leader Moammar Gadhafi was published Wednesday in the French newspaper Le Figaro. The newspaper said France did not alert allies.
The account said weapons included rocket launchers and anti-tank missiles, but French officials would only confirm light arms and ammunition were dropped to the rebels, the BBC said.
The decision reportedly was made after an April meeting between French President Nicolas Sarkozy and the chief of staff of the Libyan rebels, Gen. Abdelfatah Younis.