The unmanned aerial vehicles were spotted Saturday night by the operator of Genkai Nuclear Power Station in the southwestern Kyushu region, the Nuclear Regulation Authority (NRA) said.
Unauthorised drone flights over and near nuclear power plants are prohibited in Japan, the NRA and police said.
"No abnormalities were detected after the incident was reported, while drones have not been found inside the premises of the power plant," a spokesman for the NRA told AFP.
Police spokesman Masahiro Kosho said they have not located the drones and do not know who flew them or for what purpose.
Kyushu Electric Power Co operates the Genkai plant in Saga prefecture where two of its four reactors are being decommissioned.
The plant's other reactors resumed operation after strict safety standards were introduced following the 2011 Fukushima disaster, which was triggered by a devastating earthquake and tsunami in northeast Japan.
A law allowing nuclear reactors to operate beyond 60 years took effect in Japan last month, as the government turns back to atomic energy 14 years after the Fukushima catastrophe.
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