The case underlines the high stakes in exposing and tackling graft in a country that is attracting a surge of interest from investors but is considered one of the most corrupt in Asia.
Tempo's editor in chief Wahyu Muryadi said the magazine's security guards saw two men pull up on motorcycles at the Jakarta office at about 2.30 a.m. (1930 GMT).
"They then threw three Molotov bottles, bottles with petrol inside. Two of them blew up and then they disappeared on motorcycles," he said, adding no one was hurt and there was no significant damage to the building.
Police had sent a team to investigate, he said, while declining to speculate on the motive.
"I believe the police will do their best to investigate it. We are still working as usual and we are not in fear."
A police spokesman said the investigation had begun.
"The motive will be known after we capture the perpetrators. It's difficult for us to speculate on the motive," said spokesman Boy Rafli Amar.
Tempo has earned many powerful enemies through its reports on cases of suspected corruption involving politicians, businessmen and law enforcement officials.
The magazine is the subject of a defamation case lodged by police over its June edition, which features a cover story on police graft titled "The fat bank accounts of police officers," accompanied by a drawing of a policeman leading three piggy bank money boxes on leashes. The English-language Jakarta Globe newspaper reported on Tuesday that President Susilo Bambang Yudhoyono had instructed the national police chief to investigate the Tempo report.
