"Four people died, one police officer and three civilians," AFP quoted national police spokesman Anton Charliyan as saying Thursday.
Separately, police said four suspected attackers had been killed, including two of them who had blown themselves up, and four others arrested.
Indonesian President Joko Widodo called the blasts "acts of terror," saying he had ordered a huntdown and capture of the perpetrators and those in their network.
According to an official Jakarta police Twitter account, one explosion went off outside a shopping center called the Sarinah mall.
Gunshots were heard as police approached after the mid-morning explosion in the area that also has many luxury hotels, embassies and offices.
Charliyan said the gunfire had stopped but the attackers were still on the run, and police feared there would be more gunshots.
The shooting was reportedly happening outside a Starbucks opposite the shopping center.
Witnesses, quoted by the Associated Press, said the explosion was caused by a bomber, but there was no immediate confirmation of the claim.
A local television said that a total of six explosions had been heard.
There was no immediate word on who was behind the attacks.
Indonesia has been on alert over the threat of attacks by Takfiri groups and police have launched a crackdown on people with suspected links to the extremists.
About 150,000 police officers and soldiers were deployed during New Year's Eve to guard churches, airports and other public places.
More than 9,000 police were also deployed in Bali, the site of Indonesia's deadliest terror attack, which killed 202 people in 2002.