Under the peace deal, Kurdistan Workers Party (PKK) fighters should cross from Turkey, where they have been fighting for Kurdish rights for three decades, into Iraqi Kurdistan.
Iraqi Kurds were involved in the talks with Turkey.
The Iraqi Foreign Ministry said in a statement that the presence of armed Kurdish groups could be used "to impact the security and stability of Iraq or neighboring states."
Baghdad, however, has little control over its autonomous Kurdish region.
As well as controlling Iraq's border with Turkey, the Kurdistan Regional Government is fiercely defensive of its internal boundary with the rest of the country run by Baghdad.