The Zaporizhzhia nuclear plant was taken over by Russian forces in March 2022, one month after Moscow launched its invasion of Ukraine, and its six reactors have been shut down.
As the plant is now manned by staff who have taken Russian nationality, it was not clear how many people are affected by the new order.
But fierce fighting in the area and power cuts have raised international concerns as the plant still needs electricity and water to cool its systems.
IAEA head Rafael Grossi is to visit the site next week after holding high-level talks on Tuesday in Kyiv, the agency said in a statement.
During his visit, Grossi will "raise the crucial issue of staffing" at the plant to seek "further information" on the latest announcement.
"It is of crucial importance that the plant has the qualified and skilled staff that it needs for nuclear safety and security," Grossi said in the statement.
"The number of staff has already been reduced significantly since the war began," he added.
A source in Energoatom told AFP that Russia had been "imposing" citizenship on the plant's employees and forcing them to sign contracts with Russian-installed operator Rosatom.
"The Russians have set several deadlines. If someone does not take a Russian passport and sign contracts, they will no longer come to work," the source said.
The latest deadline was 1 January 2024, it said.
Before the war, there were 11,500 staff at the plant. At present 4,500 people are employed by the Russian operator at the plant and 940 applications were "under consideration".
Staff working at the site consist of former Energoatom employees who have "adopted Russian citizenship and signed employment contracts with the Russian operating entity", the IAEA statement specified.
Besides that "staff who have been sent to the ZNPP from the Russian Federation" work there.
The IAEA has repeatedly warned of persistent nuclear safety and security risks at the site.
IAEA officials have been on the ground monitoring the plant since September 2022.
The six reactor units, which before the war produced around a fifth of Ukraine's electricity, have been shut down.
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