No one was injured in the incident, said Jakarta police spokesman Argo Yuwono.
A patrolling police officer saw fire at the rear terrace on the second floor and immediately informed police who were guarding the embassy.
"We are still trying to catch the perpetrator," Yuwono told AFP.
Indonesians are becoming inreasingly concerned at the treatment of the Rohingya, a stateless Muslim minority in mainly Buddhist Myanmar.
Some 60,000 refugees, mostly Rohingya, have poured into neighbouring Bangladesh since the latest round of fighting broke out nine days ago when Rohingya militants attacked security instrallations.
Myanmar's army says nearly 400 people have died, among them 370 Rohingya militants.
Dozens of people on Saturday protested outside the Myanmar embassy in Jakarta, demanding that Myanmar end the crisis. They called on the Nobel Prize committee to withdraw the peace prize awarded to Myanmar's leader Aung San Suu Kyi in 1991.
Several groups protested in Jakarta's Buddhist area on Sunday.
Last November Indonesian police arrested a militant linked to the Islamic State group who was accused of plotting to bomb the Myanmar embassy.
In 2014 an Indonesian court jailed an Islamic extremist bomb-maker for seven-and-a-half years for his role in a plot to attack the embassy to avenge the killing of Rohingya.//AFP