The shallower an earthquake is, the more destructive its effects on the surface tend to be.
Strong aftershocks were felt in the same area, including one with a magnitude of 6.1.
Later on Saturday, a 6.9-magnitude earthquake was felt in North Sumatra at a depth of 183km.
Video taken at the port in Maumere showed large chunks of concrete breaking off the terminal building onto passengers waiting to board an inter-island ferry. Some were thrown into the sea when the gangway to a ship collapsed.
Emanuel Melkiades Laka Lena, governor of East Nusa Tenggara province, told a news conference that they were killed in their sleep by collapsing rubble.
Arnold Welianto, who lives in Talibura, a village near the coastline in Sikka, East Nusa Tenggara, said he was awoken by the “very strong shaking”, adding: “I was startled awake and immediately went to my child’s room.”
He told the BBC that many people had already fled into the hills.
“Some other residents were standing along the roadside because the sea had also receded,” he explained. “The water remained low for quite some time, so everyone panicked and ran – I went around to the community health centre, and the people there had already been evacuated.”
A tsunami warning was issued but lifted around three hours after the initial jolt when no significant sea level rise was detected.
A stream of people could be seen moving inland on motorbikes after authorities issued a tsunami warning. BNPB said 2,000 people had evacuated or relocated on their own.
It said three fatalities had been recorded in Sikka province, six in Manggarai province, and five in East Manggarai province.
At least two others had been seriously injured and 11 slightly injured, the disaster agency added.
