According to the ministry, 3,629 more people were discharged from hospitals, bringing the total number of recovered patients to 1,409,288.
The virus has spread to all the country's 34 provinces.
Specifically, within the past 24 hours, West Java recorded 997 new cases, Jakarta 977, Central Java 280, East Java 277 and Riau 265.
Meanwhile, the death toll of tropical cyclone Seroja in Indonesia's East Nusa Tenggara province has risen to 174, according to the National Disaster Management Agency on Saturday.
"The worst-hit areas are Alor, Lembata, and Adonara," the agency's head Doni Monardo said.
Indonesian President Joko Widodo has decided to relocate the affected settlement areas to safer places, with the consent of the local community.
The Meteorology, Climatology and Geophysics Agency said such extreme weather as heavy rains, strong winds and high sea waves of up to 6 meters occurred after tropical cyclone Seroja swirled in the Savu Sea, south of East Nusa Tenggara province, with a peak on April 5.
Seroja is the 10th tropical cyclone hitting Indonesia since 2008 and had the worst impact as it made landfall.
Currently, Seroja is moving away from Indonesia.
Earlier, it was confirmed that seven people were killed, another one was seriously injured, and scores of buildings were damaged after a 6.1-magnitude quake rocked Indonesia's western province of East Java on Saturday, officials said.
The earthquake struck at 2 p.m. Jakarta time (0700 GMT) with the epicentre 96 km south of Kepanjen town of Malang district with a depth of 80 km, Andry Sembiring, an official at the Meteorology, Climatology and Geophysics Agency, said.
The damage was classified from moderate to serious categories in the area. The risk assessment on the quake was undertaken in the districts of Lumajang, Malang, Blitar and Tulungagung, he said in a statement.
The earthquake also forced residents to flee home and the number of the evacuees was still under calculation, an official confirmed. - Xinhua