The Habur border gate is in Turkish hands, while the Ibrahim Khalil gate on the Iraq side is in the control of Iraqi authorities, Turkish Prime Minister Binali Yildrim announced.
The northern Iraq border crossing was previously operated on the Iraqi side by the Kurdistan Regional Government. It is the only point of access between Turkey and Kurdistan.
Turkish and Iraqi troops, practicing joint training exercises since mid-September, moved to the border crossing on Tuesday, the Ankara-run Anadolu Agency reported.
The Iraqi government seeks control of all travel in and out of Kurdistan -- part of a strategy to remove power from Kurdistan's autonomous government. It was prompted by a September referendum, regarded as illegal by Iraq and widely opposed by the global community, in which voters overwhelmingly chose Kurdish independence from Iraq.
The change in command on Tuesday was denied by the chief of the Ibrahim Khalil crossing. Samal Abdulrahman said no military deployment occurred, and traffic through the crossing was proceeding normally, the Kurdish Rudaw News reported.