The tsunami, which hit coastal areas of Java and Sumatra, was triggered by a volcanic eruption, RTE reported.
People have started to leave the areas most affected, amid warnings that there could be a second tsunami.
Rescue workers searched through the night for people trapped or missing after the natural disaster.
Spokesman for the Indonesian Disaster Agency, Sutopo Purwo Nugroho stated that "the number of victims will continue to rise".
Hundreds of buildings were destroyed by the wave, which slammed into the coast of Southern Sumatra and the Western tip of Java about 9.30 pm local time on Saturday after a volcano known as the "child" of Krakatoa erupted.
According to Indonesia's geological agency, Anak Krakatoa had been showing signs of heightened activity for days, spewing plumes of ash thousands of metres into the air.
The vast archipelago nation is one of the most disaster-prone nations on earth due to its position straddling the so-called Pacific Ring of Fire, where tectonic plates collide.
Tsunamis triggered by volcanic eruptions are relatively rare, caused by the sudden displacement of water or "slope failure", according to the International Tsunami Information Centre.
Unlike those caused by earthquakes, which trigger alert systems, these tsunamis give authorities very little time to warn residents of the impending threat.