"Bolton's statements in Israel are unacceptable, I can not swallow that," Erdogan said in a speech in parliament. "Bolton has made a grave mistake, and if he thinks that way, he has a big mistake and we will not compromise."
US President Donald Trump announced late last month that the US has defeated ISIS in Syria and its 2,000 troops would be taken out of the country.
But Bolton, who is currently on a four-day trip to Israel and Turkey, seemed to add several circumstances to Trump's announcement and said at the weekend that the withdrawal will depend on ISIS being prevented from reviving and obtaining security guarantees from the Turks for US-backed Kurdish militants in Syria.
Turkey is considering several Kurdish groups, including the People's Protection Groups, also known as YPG's terrorist organizations The YPG is the backbone of the Syrian Democratic Armed Forces, which is the main US partner in the battle against IS and has been controlling a large region of northern Syria for several years.
Trump's initial announcement of the retreat was made by American allies, not least the Kurds, blind, but was praised by Erdogan, who in January in the north Syria started an operation to clear the border area of the Kurdish fighters.
At the end of December, the YPG announced it was withdrawing from the city of Manbij and urged Syrian government forces to protect the area from a Turkish attack.
"We have completed our military preparations, and we are determined to take action against YPG, and we will soon be doing away with the abolition of terrorist groups in Syria," Erdoğan said Tuesday.
Garrett Marquis, spokesman for the US National Security Council, said in a statement that Bolton had had a "productive discussion" with Erdogan's senior advisor Ibrahim Kalin on Tuesday.
"They had a productive discussion on the President's decision to retreat at a reasonable pace from Northeastern Syria, recognizing other topics for dialogue and emphasizing the close bilateral relations between the US and Turkey," Marquis said.
"The US looks forward to today's military-to-military consultations on our cooperation in Syria."