National Police spokesman Setyo Wasisto said three officers had been killed, and that examination of the scene had shown that there appeared to have been two suicide bombers, not one as originally thought.
Five officers and five civilians were wounded, he said.
Indonesia has suffered a series of mostly low-level attacks by Islamic State sympathizers in the last 17 months, but Wasisto said police had not confirmed any Islamist motive for Wednesday's bombing.
"The police officers were on duty to guard a group of people who were holding a parade. The parade hadn't passed yet when the blast happened," Wasisto told a news conference.
"The two suspects were both male. Their identities will be released later," he said.
Wasisto said the explosives appeared to have been packed into pressure cookers. A similar bomb was used in February in the city of Bandung by a lone attacker, killed by police, whom authorities suspected of having links to a radical network sympathetic to Islamic State.
Authorities in the world's biggest Muslim-majority nation are increasingly worried about a surge in radicalism, driven in part by a new generation of militants inspired by Islamic State.
In January 2016, four militants killed four people in a gun and bomb assault in the heart of Jakarta.
While most of the attacks since then have been poorly organized, authorities believe about 400 Indonesians have gone to join the militant group in Syria, and could pose a more lethal threat if they come home.
On Wednesday night, heavily armed police cordoned off the area around the bus station with tape to hold back hundreds of onlookers while bomb disposal officers with protective suits examined the area.
Transport Minister Budi Karya tweeted that he had asked staff to increase vigilance on the city's transport network.
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24/05/2017
20:26
Two blasts rocked a public transport terminal in the Indonesian capital Jakarta today and caused casualties, police said.
“There were two blasts at around 9:00 PM (1930 IST), close to each other, there are three victims,” East Jakarta police chief Andry Wibowo told TV station MetroTV, without saying whether the victims had been killed or injured.
“From the damage I can see the explosions were pretty big.” It was not immediately clear what caused the blasts at the Kampung Melayu terminal, which is served by mini-vans and buses.
TV pictures showed smoke rising from the terminal and police rushing to carry casualties away from the scene. Large numbers of police officers were at the scene and had cordoned it off.
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