The comments, by Nasr bin Ali al-Ansi, came in a video response to questions by reporters posted on one of the group's Twitter accounts.
It appeared to have been recorded before Saturday's killing of two hostages an American and a South African during an attempted US rescue from al-Qaida militants. Both groups regularly execute prisoners but beheadings and other brutal acts have become a trademark of IS.
IS extremists initially fought to oust Syrian President Bashar Assad. But other groups, including al-Qaida central command, denounced them as too violent. The group now controls large swaths of Iraq and Syria.
Al-Ansi said that previous beheadings by al-Qaida in Yemen were "individual acts" and were not endorsed by the leadership. He appeared to be referring to the beheading of 15 Yemeni soldiers by suspected al-Qaida militants in August.
"Filming and promoting it among people in the name of Islam and Jihad is a big mistake and not acceptable whatever the justifications are," al-Ansi said. "This is very barbaric," he added.
Al-Ansi said that the drone strikes stoke popular outrage that boosts al-Qaida's popularity.
"While they kill some of the jihadis, the US drone strikes increase the sympathy of Muslims with us," he said, adding: "thanks to the blood of the martyrs, the call for jihad spreads.
