There were no immediate reports of major damage or injuries from the quakes.
The Meteorological Agency issued a tsunami advisory for southwestern Japan after an earthquake with preliminary magnitude 6.7 struck at 10:46 a.m. (0146 GMT).
The notice covered islands around Miyakojima, part of the Ryukyu island chain that stretches southwest toward Taiwan.
A tsunami advisory is used when waves are forecast to be no more than 18 inches tall, agency official Yuji Nishimae said. The agency issues a warning when the waves are forecast to be 3.1 to 6.2 feet high, and warns of a large tsunami when higher waves are expected, he added.
The agency lifted its advisory at 11:50 a.m. (0250 GMT). No tsunami was detected, agency official Kana Akiyama said.
The 6.7-magnitude quake came a little more than an hour after a tremor with a preliminary 6.2 magnitude quake struck the same area. A third quake, also with a preliminary 6.2 magnitude, followed later in the morning.
People living on the island were warned to stay away from the coast as a precaution.
"I could feel a little bit of shaking, but it wasn't strong enough to rattle cups on desktops and the like," local policeman Takumi Higa said.
Japan is one of the world's most earthquake-prone countries because it sits atop four tectonic plates. A magnitude 5.5 earthquake jolted northern Japan early Thursday, but there were no reports of injuries or damage.
Miyakojima, part of Okinawa prefecture, is about 1,130 miles southwest of Tokyo.