He said airports in the Kurdish region will be under the command of the Federal Ministry of Interior.
"There is no truth in reports about an agreement between the central government and KRG on demarcating border and return of Peshmerga forces", he said.
In a statement, al-Abadi's office said flights will be resumed to the Erbil and Sulaymaniyah airports after a six-month suspension.
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Baghdad imposed the blockade in September after Iraqi Kurdistan voted for independence in a non-binding referendum.
Iraqi Prime Minister Haidar al-Abadi announced on Tuesday that the Baghdad government was ending its almost six-month air blockade on Iraqi Kurdistan.
It also specified that the biometric system used in the Kurdistan Region's airports will be linked with the federal system.
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The announcement comes some six months after the airports were initially shut to worldwide flights following a controversial referendum vote in northern Iraq's self-ruled Kurdish region that overwhelmingly backed independence from Baghdad.
Erbil and Baghdad have long-standing issues dividing them, including the Kurdistan Region's budget share, conflicts over the administration of disputed territories, and the distribution of oil export revenue.
Arbil had already agreed to that and control of airport security was the last stumbling block, an official told AFP at the end of February when the blockade was extended for another three months.
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Iraq's neighbouring countries, especially Turkey, Iran and Syria, fear that the Iraqi Kurds' pursuit of independence threatens their own territorial integrity by inspiring the Kurdish population in those countries to seek independence. Late a year ago, following the failed independence push, federal forces recaptured the oilfields, severing a key financial lifeline for the Kurds.