Erdogan said that the Syrian Kurdish party the Democratic Union Party (PYD), which has been leading the defence of Kobane, fears losing its influence in northern Syria when the peshmerga arrive in the coming days.
His comments underlined the extent of Turkey's animosity towards the PYD, which Erdogan described as a terror group linked to Kurdish militants in Turkey.
"The PYD does not want the peshmerga to come," Erdogan said in comments published by newspapers including the Milliyet and Hurriyet dailies.
"They don't want the peshmerga to come to Kobane and dominate it," he told reporters returning on his presidential plane after a visit to Estonia.
"The PYD thinks its game will be spoilt if the peshmerga come. Their scheme will be ruined," he said.
He said that the peshmerga had been willing to send some 500 fighters as a first deployment but this had been reduced to 155 at the insistence of the PYD, who were even reluctant to accept this number.
Turkey last week unexpectedly announced that it will allow peshmerga fighters from the Kurdistan region of northern Iraq to cross its territory to join the fight for Kobane.
However the deployment has yet to take place and what relationship the peshmerga will have with the PYD on the ground remains to be seen.
Ankara has long accused the PYD of failing to distance itself from Syrian President Bashar al-Assad and being the Syrian arm of the Kurdistan Workers Party (PKK), which has waged a three-decade insurgency for Kurdish self-rule in Turkey.
"The PYD is a terror group just the same as the PKK," said Erdogan.
In contrast to its acrimonious ties with the PYD, Ankara has in recent years built up a close relationship with the regional authorities in Iraqi Kurdistan, who control the peshmerga.
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- 'Game within a game' -
Erdogan said last week that the peshmerga would be joined in the defence of Kobane by 1,300 fighters from the anti-Assad Free Syrian Army (FSA).
He hailed the expected arrival of the FSA as a "beneficial step" which would spoil the PYD's "scheme and trap" in Kobane.
"The PYD is not sincere," he said.
Erdogan expressed suspicion over the intentions of the parties in the Kobane crisis, which he described as a "game within a game" involving an unspecified "higher mind" other than the PYD.
"The game being played out at our borders is not a random game. It is also not a simple game," he said, without specifying further.
Erdogan said he could not understand the strategic value of Kobane for the United States, attacking Washington for now devoting so much attention to the town after it had looked on as IS captured swathes of Iraq and Syria earlier in the year.
He also waded into a controversy about the origins of Kobane, which is known as Ain al-Arab to the Arabs and Kobane to the Kurds.
"It is Ain al-Arab as the name implies. Later it has turned into Kobane."