The spill has affected at least 13 villages, threatening the livelihoods and health of thousands of people.
Rescue efforts were complicated by the boat's manifest listing only 111 passengers, officials say.
It is not immediately clear how long the disruption might last, though it appears to have affected most areas of Jakarta.
Indonesia's Meteorology, Climatology, and Geophysical Agency says the early tsunami warning in Java has ended.
Some 15 people are reportedly dead after a ferry sinks off near Madura Island, near Java in Indonesia.
Landslides are common in Indonesia, a vast tropical archipelago prone to natural disasters and torrential downpours.
The landslides buried 30 homes.
Some 584 people have been injured and hundreds of homes and other buildings heavily damaged.
Java is an old-fashioned brew dating back to the colonial period when few locals could afford bean-extracted coffee.
A string of earthquakes in Lombok in eastern Indonesia killed more than 550 people over the summer.
The area covered by the expedition included a long stretch of the Indian Ocean off Java's southern coast, as well as the Sunda Strait.
The Citarum Basin supports 28 million people, but is called by many the dirtiest in the world.
Those missing were farmers in a rice field who were tending to their crops at the time of the landslide.
The result of the painstaking 15-minute process is a 10,000 won (US$8.71) cup of cold coffee that has won Lee thousands of fans at his cafe and online.