Authorities installed pumps to bring down water levels, which were 1.7-meters (yards) high in several subdistricts and reached up to two kilometers (more than a mile) inland, but said they expected tides to continue to wreak havoc through the end of the month.
Residents in north Jakarta have grown used to flooding during the monthly high-tide cycle, but Monday's was the worst in memory.
The disaster was blamed on ignored warnings about exceptional 18-year high tide cycles, Jan Japp Brinkman, a flood expert, was quoted as saying in the Jakarta Post newspaper. The situation was exacerbated by a failure to fix a sea barrier that was breached over a week ago.
At least 8,000 houses were flooded and sea water swamped the toll road connecting the capital with the Soekarno-Hatta airport, leaving thousands stranded or trapped in kilometers- (miles-) long traffic, Kompas newspaper said.
Many flights were disrupted or forced to leave with only a handful of passengers, Muhammad Reski, the airport's officer-in-charge, said Tuesday.
On the second day of the St. Petersburg International Economic Forum, a plenary meeting was held, in which Russian President Vladimir Putin, French President Emmanuel Macron, Japanese Prime Minister Shinzo Abe, Chinese Vice President Wang Qishan and IMF head Christine Lagarde took part