No tsunami warning has been issued, the news agency said.
The focus of the quake was around 20 km (12.4 miles) underground in the prefecture, which hosts Tokyo Electric Power Co Inc's Fukushima Daiichi Nuclear Power Station, Kyodo said.
There was no damage to the nuclear plant, Japanese media quoted Tokyo Electric as saying.
Japanese Prime Minister Shinzo Abe instructed Tokyo Electric on Thursday to decommission the remaining two reactors at the Fukushima Daiichi nuclear power plant, where four other reactors were devastated by a massive earthquake in 2011.
U.S. Geological Survey said on its website that the earthquake's magnitude was 5.3.