Some 600 militants were allowed to leave as part of a deal, negotiated by Lebanon's Hezbollah, in exchange for identifying the location of the remains of Lebanese soldiers captured by IS in 2014, and later killed.
The deal has provoked controversy in Lebanon, as some have voiced opposition to negotiations with the militants.
It has also angered Iraqis who expressed resentment at the deal that effectively puts the militants on their border.
"Any deals or understandings between the warring parties inside Syria or in the region must take into consideration the security of Iraq and not to lead to anything that poses any threat to our national security," the Iraqi government spokesman, Saad al-Hadithi, told The Associated Press . Al-Hadithi said the Iraqi government "will firmly face any threat to Iraqi territories."
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Some Iraqis also expressed resentment on social media. "Who's going to pay for the delivery sent by Hassan Nasrallah to us?" wrote well-known writer Saleh al-Hamdani on his Facebook page, referring to Hezbollah's leader. "Will Hashed (Shiite militias) or Federal Police or Counter Terrorism Forces pay for it?"
Daesh is the Arabic acronym for IS.
The Lebanese government and Hezbollah have both defended the deal that allowed IS safe passage to the eastern province of Deir el-Zour, an IS stronghold, saying it was the only way Lebanon could uncover the fate of its kidnapped soldiers and recover their remains.
IS' departure leaves the border between Syria and Lebanon free of Sunni militant extremists for the first time in years. Syrian state-run news agency SANA said the buses carrying the militants arrived Tuesday to a handover point in the town of Hamimiyah in the eastern Deir el-Zour province. They are expected to continue from there to the town of Boukamal, near the Iraqi border.
Salaheddin reported from Baghdad.