The magazine`s editor-in-chief, Wahyu Muryadi, said later two of the bombs exploded and one did not.
"The perpetrators who rode on a motorbike from the eastern to western direction threw three Molotov bombs from outside the fence," he said.
The bombs did not cause any damage nor casualty because they landed in the building`s parking lot, he said.
"The fire from the bombs was put out by the office`s security guards immediately," he said.
The incident happened when the office was almost deserted as no printing process was going on.
Tempo has reported the incident to the Jakarta Police office and the Matraman Metro police sector for investigation.
"About the motive, let us wait until the police officers find out. I really don`t know why someone should want to threw Molotov bombs at our office," he said.
Tempo`s latest edition ran stories covering suspicious bank accounts of high-ranking police officers as its cover story.
The magazine reported that at least seven high-ranking police officers were hoarding billions of rupiah in their bank accounts, transferred from third parties.
The National Police said it was planning to file a lawsuit against Tempo magazine over the stories.
Meanwhile, President Susilo Bambang Yudhoyono has ordered National Police Chief (Kapolri) Bambang Hendarso Danuri to tackle the case of several Police top officers reported to have huge amounts of money in their bank accounts.
Speaking before chairing a limited cabinet meeting at his office here on Monday (July 5), the President said the police chief should make every possible effort to check the truth of the report and, if it was true, to clarify the matter and prevent the recurrence of similar cases.