The 7.7-magnitude quake struck in the Mentawai Islands area west of Sumatra late Monday, generating waves as high as three metres (10 feet) that swept away 10 villages.
Hendri Dori Satoko, a lawmaker in the Mentawai Islands, told MetroTV: "Our latest data from the crisis centre showed that 108 people have been killed and 502 are still missing."
Disaster Management Agency spokesman Agolo Suparto said: "Ten villages have been swept away by the tsunami."
The missing included a group of Australian surfers, though Australian media reports later suggested they had been found safe and well.
Health Ministry Crisis Centre head Mudjiharto said the Mentawai waves reached up to three metres high and waters swept as far as 600 metres (yards) inland on South Pagai island, the hardest hit.
"Eighty percent of buildings in Muntei village have been damaged by the waves and many people are missing there," Mudjiharto said.
He said medical personnel were on their way to the worst-hit areas in helicopters but rescue efforts had been hampered by disruption to communications in the region.
There are no commercial flights to the island and travelling by ferry from Sumatra can take at least half a day.
Indonesia sits on the Pacific "Ring of Fire" and the archipelago is frequently struck by powerful earthquakes, including one of 7.6 magnitude in September last year in Padang that killed about 1,100 people.
The 2004 Asian tsunami -- triggered by a 9.3-magnitude quake off Sumatra -- killed at least 168,000 people in Indonesia alone.
Rescuers have launched a search for a boat believed to be carrying a group of nine Australians and a Japanese national that has been missing since the quake.
It was reportedly not equipped with a satellite telephone but SurfAid International's Dave Jenkins said its Australian captain had "been around here for a long time. He knew to contact in if he could. So that's why we're extra concerned."
Disaster Management Agency aid coordinator Wisnu Wijaya told AFP that rescue teams from capital Jakarta would join forces with local teams to evacuate bodies and deliver food aid, medicines, tents and blankets.
"We'll leave early in the morning from Jakarta," he said, adding that a cargo flight would carry four tonnes of medicines and food.
A group of Australian tourists reported that their boat with 15 people aboard was destroyed by a "wall of white water" crashing into a bay after the undersea quake and said some had to cling to trees to survive.
"We felt a bit of a shake underneath the boat... then within several minutes we heard an almighty roar," said Rick Hallet, an Australian who operates a boat-chartering business in Sumatra.
Hallet recounted his group's ordeal when the quake struck, with some climbing trees to survive.
"The bay we were in was several hundred metres across and the wall of white water was from one side to the other, it was quite scary," he told Fairfax Radio Network.
Another boat was anchored next to them, he said.
"The wave picked that boat up and brought it towards us and ran straight into us and our boat exploded, caught on fire, we had a fireball on the back deck and right through the saloon within seconds.
"I ordered everyone up to the top deck to get as high as possible, then the boat exploded and we had to abandon ship," he told Australia's Nine Network.
The group jumped into the water, some of them being swept 200 metres inland, and took shelter by climbing trees, waiting for 20 minutes to half an hour until the surges passed.
Eventually all the group were accounted for, he said.
Residents reported shaking as far away as the West Sumatran provincial capital of Padang when the main quake struck.
The undersea quake hit at 9:42 pm (1442 GMT) at a depth of 20.6 kilometres (12.8 miles), 280 kilometres south of Padang, the US Geological Survey said. It was followed by strong aftershocks.