The survivors were rescued by nearby boats.
Indeed, the popularity of Lake Toba is such that the Indonesian government has taken special care to try and introduce sustainable tourism measures out of fear that the high level of visitors may be destroying its natural majesty.
Maher Tamba, an official with the local disaster agency, said at least half a dozen vessels were searching for survivors.
"We believe there was a waterspout that generated strong winds and waves that destabilized the boat and caused a panic", he told reporters. It released the names of 94 people confirmed as missing but said the figure is expected to rise as information from relatives is compiled. "In many occasions, I often remind to not carry passengers beyond the ship capacity", he said.
A search and rescue team heads out looking for missing passengers who were on a ferry that sank in Lake Toba, at Tigaras Port, Simalungun, North Sumatra, Indonesia, June 19, 2018.
Among the grief-stricken relatives waiting by the shore was Juwita, a survivor who lost hold of her child in the confusion.
She added: "I wanted to grab my child but I couldn't".
Indonesian rescue workers struggled in rain and two-meter waves on Tuesday to search for at least 128 passengers from an overloaded ferry that sank in Lake Toba, a tourist destination in an ancient supervolcano crater on Sumatra island.
Since Friday, the Muslim-majority nation has been celebrating the festival of Eid, with millions now on vacation around the country.
It is one of the deepest lakes in the world and covers some 1,145 square kilometres (440 square miles).
Ferry accidents are common in Indonesia - a 17,000 island archipelago nation where many rely on boats to get around.
Last week, a traditional wooden boat with about 40 people capsized in the island of Sulawesi, killing more than a dozen people. Ferries run back and forth from the island to towns on the lake's shore.
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