There were no immediate reports of damage or casualties.
The 6.0-magnitude quake was centered 25 miles beneath the Sunda strait, the U.S. Geological Survey said on its Web site, and struck 90 miles southwest of Jakarta.
Suharjono, head of the earthquake division at Jakarta's meteorological agency, told Metro TV that based on the initial estimate of Wednesday's quake strength, it was not strong enough to trigger a tsunami.
But he urged people to be on guard.
On Monday, a tsunami triggered by a magnitude 7.7-earthquake slammed into Java's southern coast, killing 531 people and leaving more than 270 missing. A series of strong aftershocks have rattled the region since then.
Meanwhile, rumors of another killer wave sparked mass panic Wednesday in the town hardest hit by the tsunami, and amateur video that captured some of the horror of the disaster surfaced.
The video shows children playing in the surf and building sandcastles followed by brief footage of a wall of black water bearing down on the beach in Pangandaran. The camera person then runs away amid screams.
The tsunami smashed into a 110-mile stretch of Java island's coastline, which was unaffected by the devastating 2004 Asian tsunami.
The waves, more than 6 feet high, reached 200 yards inland in some places, destroying scores of houses, restaurants and hotels. Cars, motorbikes and boats were left mangled in fishing nets, furniture and other debris.
It was unclear how Wednesday's rumor of another tsunami spread, but it caused mass panic among the town's traumatized residents. More than 1,000 people ran from the beach area or jumped on bikes or in cars and headed inland amid shouts of "The water is coming!"
"People suddenly started running so I joined them," said Marino, a 42-year-old man who was caught up in the exodus.
Police and army teams with sniffer dogs and mechanical equipment kept searching for survivors of the tsunami, but found only bodies amid the ruins, pushing the death toll to 531, said Maman Susanto, from the government's national disaster coordinating board. Several foreign tourists were among the dead.
He said 275 people were listed as missing.
At the area's main hospital, in the town of Banjar, medics treated a steady stream of patients, most from the Pangandaran coast. Some slept on dirty mattresses on the floor, while others were treated in the admissions hall.
Surgeons amputated the left leg of a women who was trapped under the rubble of her house.
"I thought I was going do die, but God gave me mercy so I can carry on with my life," Tintin Rotiyani said from her hospital bed.
The Hawaii-based Pacific Tsunami Warning Center and Japan's Meteorological Agency issued warnings of a possible tsunami about 15 minutes after Monday's quake. The tsunami struck Java about 45 minutes later — before authorities had time to warn anyone on the coast.
Science and Technology Minister Kusmayanto Kadiman appeared to back away from comments made Tuesday that the government received both regional tsunami bulletins, but did not attempt to announce the warnings.
He told el-Shinta radio that the government's meteorological agency sent text messages to at least 400 officials and one of his staffers appeared on national television to warn of the tsunami.
But Kadiman did not say whether the actions were taken before the tsunami hit, or whether the 400 officials lived on the threatened coastline.
Moreover, with no warning sirens or alarms on the beaches, getting the message to significant numbers of residents and tourists would likely have been impossible.
The quake was not felt by most people on the beaches. The first most people knew of the wave was when they heard screams of "Tsunami! Tsunami!"
Indonesia was hardest hit by a 2004 tsunami that killed at least 216,000 people in a dozen Indian Ocean nations — with more than half the deaths occurring in Sumatra island's Aceh province.
Though the country started to install a warning system after that disaster, it is still in the early stages. The government had been planning to extend the alert system to Java in 2007.