The victims comprised a nine-year-old girl and two men, Japanese broadcaster NHK reported.
The earthquake was recorded at 7.58 a.m. and had its hypocenter at about 13 km depth in Osaka Prefecture on the island of Honshu, the largest in the Japanese archipelago, according to the Japan Meteorological Agency (JMA).
However, no tsunami warning was issued, reports Efe news.
Several buildings in Osaka and Takatsuki collapsed and were on fire.
Railway services in Osaka, Shiga, Kyoto and Nara, both high speed bullet trains and local rail services, were halted.
Osaka’s Kansai Airport has been shut down while its runways were being checked for damage.
The authorities said that none of the 15 nuclear reactors in this region have been affected by the quake.
The Japanese government has set up a task force to gather information related to the strong earthquake and the Chief Cabinet Secretary, Yoshihide Suga, called on citizens to keep an eye on developments through the media.
Around 170,000 houses in Osaka prefecture are experiencing power outages following the quake, NHK reported.
According to the JMA, this is the first time that the Osaka prefecture has seen an earthquake of this intensity since 1923.
Japan sits on the so-called Ring of Fire, one of the most active seismic zones in the world, and experiences earthquakes frequently, which is why most infrastructure is specially designed to withstand earthquakes.