In an indication of the tensions that remain between Washington and and Ankara on how to deal with the Islamic State group, Erdogan said he could not understand why Kobane was so strategic for the United States.
He said the weapons had fallen into the hands of the Democratic Union Party (PYD) - a Syrian Kurdish group that Ankara does not support - and also IS jihadists.
"It has become clear that this was wrong," Erdogan told reporters at Ankara airport before leaving on a trip to Latvia and Estonia.
The Syrian Observatory for Human Rights monitoring group said at least one of the loads dropped had been picked up by the jihadists. A video purportedly showing this has surfaced online.
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But Erdogan indicated that Turkey was equally troubled by the weapons falling into the hands of the PYD, whose armed branch the People's Protection Units (YPG) has led the fight against the jihadists.
Ankara sees the PYD as the Syrian arm of the Kurdistan Workers' Party (PKK), whose armed campaign for self-rule in Turkey's southeast has left 40,000 people dead over three decades.
"Any support you would give PYD would benefit the PKK. And as Turkey we need to fight against this," Erdogan added.
"One should not resort to such actions for appearances' sake," he said of the airdrops.
Turkey's animosity towards the PYD puts it at odds with the United States, which favours supporting the group to fight the jihadists and says it should not be equated with the PKK.
Ankara has insisted it shares the West's abhorrence of IS but also wants a comprehensive strategy to bring down Syrian President Bashar al-Assad after the three-and-a-half year civil war.