A delegation including senior US diplomat Brett McGurk, special envoy to an international coalition fighting IS in Syria and Iraq, last week met members of the Kurdish People's Protection Units (YPG), a powerful militia that is in control of Kobane.
The meetings come after the YPG's political wing, the Democratic Union Party (PYD), was excluded from new peace talks in Geneva being organised by the UN. Ankara had threatened to boycott the talks if PYD was invited.
"He visits Kobane at the time of the Geneva talks and is awarded a plaque by a so-called YPG general?" Erdogan told reporters on his plane returning from a trip to Latin America and to Senegal.
"How can we trust (you)?" Erdogan said.
"Is it me who is your partner or the terrorists in Kobane?"
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His comments were carried by Turkish media on Sunday.
Ankara considers the PYD and YPG to be affiliates of the outlawed Kurdistan Workers Party (PKK), which has waged an armed insurgency in Turkey, while Syria's opposition accuses them of being too close to the regime in Damascus.
But the coalition has worked closely with the YPG since it launched air strikes in Syria in September 2014, expanding a campaign that began in Iraq a month earlier.
"Do you accept the PKK as a terrorist organisation? Then why don't you list the PYD and the YPG as a terrorist organisations, too?" Erdogan asked on the plane.
Kurdish forces backed by coalition air strikes ousted IS fighters from Kobane after a months-long struggle in January last year.
Turkey fears the creation of an autonomous Kurdish region in Syria -- similar to the Kurdish region in northern Iraq -- would spur the separatist ambitions of Turkey's own Kurds.
The PKK is blacklisted as a terrorist organisation by Turkey and much of the international commnunity.