The Iraqi government has chose to reopen the airports of Erbil and Sulaymaniyah, a report in Saudi Press Agency said.
In September 2017 people in the semi-autonomous Kurdish region of northern Iraq voted in the controversial referendum, despite warnings from the central government in Baghdad and global opposition.
The move "aims to facilitate the travel of citizens" through the two airports, the statement said.
Government spokesman Saad al-Hadithi said the airports are due to open within a few days.
"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.
The passports and national ID offices and the employees at the airports of Erbil and Sulaimaniyah will also be linked to the federal Interior Ministry, it added.More news: PM Modi launches TB Free India Campaign
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It was not immediately clear whether the region would continue to maintain its independent visa system.
"The opening of Kurdish airports to worldwide flights is an important step", Nechirvan Barzani, the prime minister of the Iraqi Kurdistan region, told a news conference, according to Kurdish Rudaw TV.
Since the flight ban went into force, all Kurdistan-bound global flights have been rerouted to Baghdad, which also imposed entry visas to foreigners wishing to visit the Kurdish region.
Ties between Erbil and Baghdad have substantially deteriorated after the last year's referendum on independence in the Kurdistan Region, which saw overwhelming majority favoring statehood.
The flight ban was part of a battery of penalties inflicted on the Kurds as Baghdad sought to nullify the poll, with federal forces also seizing disputed oil-rich regions.
Baghdad and Arbil have been engaged in a political and territorial struggle since the September 25 independence referendum.