Police suspected a suicide bomber was responsible for at least one of the blasts and up to 14 militant gunmen were involved in the attack.
Indonesian police shot dead four suspected militants who were part of a bomb and gun attack in the capital, Jakarta, on Thursday and the area is being secured, a police spokesman said.
"We are sterilising the building from basement to top," Iqbal Kabid told reporters, explaining that a gunbattle between the attackers and police took place in a cinema that is in the same building as a Starbucks cafe that was attacked.
"We will declare the situation secure soon," he said.
One blast was in a Starbucks cafe and security forces were later seen entering the building.
"The Starbucks cafe windows are blown out. I see three dead people on the road. There has been a lull in the shooting but someone is on the roof of the building and police are aiming their guns at him," said a Reuters photographer.
Police suspected a suicide bomber was responsible for at least one of the blasts and up to 14 militant gunmen were involved in the attack, Metro TV reported.