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The point of contention is reaching an agreement over the use of a local airport, according to the Japanese Times.
Japan plans to send chartered flights to Wuhan to conduct the evacuation.
The operation was to begin early Tuesday as the number of pneumonia cases caused by the new coronavirus shot up.
A scheduling conflict involves the U.S. also planning to evacuate U.S. nationals from the Chinese city aboard a chartered flight Tuesday, the sources said.
It is reportedly the first time Japan has evacuated its nationals from a foreign country because of an infectious disease outbreak, according to the Japan Times.
Two or three flights to Wuhan are planned once an agreement is reached.
As of Friday, there were about 710 Japanese registered in the province, according to the Japanese government.