Iran, which borders Iraq and the autonomous Kurdish region, strongly opposed the vote held on Monday, fearing it would provoke separatists among its own Kurdish population.
Iraq's central government has demanded the annulment of the referendum, which resulted in a huge "yes" for independence.
"A joint military exercise between Iran's armed forces and units from the Iraqi army will be held in the coming days along the shared border," Iranian Armed Forces spokesman Masoud Jazayeri told reporters.
"In the meeting, the territorial integrity and unity of Iraq and the illegitimacy of the independence referendum in northern Iraq were stressed again and necessary decisions were taken to provide security at the borders and welcome Iraq's central government forces to take position at border crossings."
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Tehran has accepted a request by Baghdad for an Iraqi army presence at border crossings.
Iraqi soldiers on Tuesday also took part in a Turkish military drill close to the Iraqi frontier.
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