Vice National Police Chief Syafruddin, who uses one name, said an initial investigation showed there were two explosions and a suspected suicide bomber had also died.
"Tonight, to Indonesian citizens and all of us who are here at the scene, I express very deep concern. There have been bomb explosions at the Kampung Melayu bus terminal and for now they are believed to have been a suicide bombing," he said.
He said the officers had been guarding a parade by a group of local people.
The explosion occurred in a parking lot next to the bus terminal in eastern Jakarta. A bomb squad was investigating the explosion as heavily armed police guarded the area.
TV channels showed people helping a victim lying on the ground, and three policemen carrying another victim away from the scene.
Indonesia, the world's most populous Muslim-majority country, generally follows a moderate form of the faith.
The government has carried out a sustained crackdown on militants since the 2002 Bali bombings by al-Qaida-affiliated radicals that killed 202 people. A new threat has emerged in the past several years from extremists who sympathise with the Islamic State group.
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