Authorities fear the toll will rise.
There have so far been no claims of responsibility, but one analyst likened the timed attacks to the Paris massacre where gunmen struck several locations at the same time.
The attack is the first major one in Jakarta since the 2009 simultaneous attacks on the J.W. Marriott and Ritz Carlton hotels, which killed seven.
With the operation to contain the attackers still going on, several things were unclear: Exactly how many gunmen were involved, and how many locations they struck.
The U.S. Embassy in Jakarta asked Americans to stay away from the area, saying the "situation continues to unfold."
One of the targets of the Thursday attacks was a police station, next to a busy shopping center, the Sarinah Thamrin Plaza.
Gunmen used grenades and engaged in a firefight with officers, Indonesian National Police spokesman Anton Charliyan said. Read more on edition.cnn.