The tsunami warning was at first issued following the 8.6-magnitude earthquake, which was later scaled down. However, the warning was issued again for two hours after the second earthquake hit the Aceh province of the country.
The tsunami watch was earlier lifted for Thailand, Myanmar, Australia and Malaysia.
The first 8.6-magnitude quake off Aceh province, hours earlier, had spawned a wave around 30 inches (80 centimeters) high but caused no serious damage.
The US Geological Survey had said the strong temblor that followed was centered 10 miles (16 kilometers) beneath the ocean around 380 miles (615 kilometers) from the provincial capital, Banda Aceh.
Harjadi, a local official who goes by only one name, said the new tsunami warning was for residents living along the western coast of the country.
It included Sumatra island and the Mentawai islands.
The Pacific Tsunami Warning Center in Hawaii said a tsunami watch was in effect for Indonesia, India, Sri Lanka, Australia, Myanmar, Thailand, the Maldives and other Indian Ocean islands, Malaysia, Pakistan, Somalia, Oman, Iran, Bangladesh, Kenya, South Africa and Singapore.
But hours later, the threat appeared to have passed.
Roger Musson, seismologist at the British geological survey who has studied Sumatra's fault lines, says the temblor was a strike-slip quake, not a thrust quake. In a strike slip quake, the earth moves horizontally rather than vertically and doesn't displace large volumes of water.
"When I first saw this was an 8.7 near Sumatra, I was fearing the worst," he said, noting one of the initial reported magnitudes for the quake. "But as soon as I discovered what type of earthquake it was, then I felt a lot better."
The tremor was felt in Malaysia, where it caused high-rise buildings to shake for about a minute, and in Singapore, Thailand, Bangladesh and India.
There was chaos in the streets of Aceh, where memories of a 2004 tsunami that killed 170,000 people in the province alone, are still raw.
Patients poured out of hospitals, some with drips still attached to their arms. In some places, electricity was briefly cut.
Hours after the temblor, people were still standing outside their homes and offices, afraid to go back inside.
There were several strong aftershocks.
"I was in the shower on the fifth floor of my hotel," Timbang Pangaribuan told El Shinta radio from the city of Medan. "We all ran out. ... We're all standing outside now."
He said one guest was injured when he jumped from the window of his room.
Thailand's National Disaster Warning Center issued an evacuation order to residents in six provinces along the country's west coast, including the popular tourist destinations of Phuket, Krabi and Phang-Nga.
India's Tsunami Warning Center issued a warning for parts of the eastern Andaman and Nicobar islands. In Tamil Nadu in southern India, police cordoned off the beach and used loudspeakers to warn people to leave the area.
Satheesh Shenoi, director of the Indian National Center for Ocean information Services, said the chance of a tsunami was diminishing.
"There are no indications of tsunami wave; the instruments are not showing any sea level change," he said.
The quake was felt in Dhaka, Bangladesh, where many people in the city's commercial Motijheel district left their offices and homes in panic and ran into the streets. No damage or causalities were reported.
In Male, the capital of the Maldives, buildings were evacuated.
Indonesia straddles a series of fault lines that makes the vast island nation prone to volcanic and seismic activity.
A giant 9.1-magnitude quake off the country on Dec. 26, 2004, triggered a tsunami in the Indian Ocean that killed 230,000 people, most of them in Aceh.
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