"The necessary measures have been taken to remove these groups from the border areas, and they have been settled in distant camps in the centre of Kurdistan," Foreign Minister Fuad Hussein told a press conference.
A year ago, Tehran launched several deadly missile and drone strikes on Kurdistan region.
The strikes came just after protests began in Iran over the death in custody of Mahsa Amini, 22, an Iranian Kurd arrested for allegedly breaching the Islamic republic's strict dress code.
Iraq's autonomous Kurdistan region hosts camps and rear bases operated by several Iranian Kurdish factions, which Iran has accused of serving Western or Israeli interests in the past.
In March, the two countries signed a "security" agreement covering their common border.
Tehran last month said that, under the deal, Iraq should disarm the groups before September 19, remove them from their bases and transfer them to camps.
"The September 19 deadline will under no circumstances be extended," and Iran will "assume its responsibility" if Iraq does not comply, Foreign Ministry spokesman Nasser Kanani said at the time.
Without raising the question of disarmament, Hussein said his country had "begun implementing the agreement" and that he would bring this message to Tehran during a visit on Wednesday.
"We expect from the Iranian side that they do not turn to violence against Kurdistan or against the sovereignty of Iraq", he emphasised.
Hussein said negotiations with Iran would focus on how "to stop these opposition groups from crossing the border and using weapons against the Iranian government".
They would also address the importance of "avoiding threats of violence, and threats of bombing certain areas of Iraqi Kurdistan".
Until now, the regional government of Iraqi Kurdistan has not spoken publicly about implementation of these measures, even though several meetings between officials of the Kurdistan region and Iran have taken place.