On Wednesday, about 300 activists from the Islamic Defenders' Front (FPI) rallied outside the building to demand that the local version of the magazine, which carries no nude photos, cease publication.
They tore up copies of the magazine and threw stones at the building, shattering windows.
One of about 90 policemen guarding the building was injured, but most of the magazine's employees had left the offices before the attack happened.
There were no immediate reports of arrests, but witnesses said some police chased stone-throwers.
Salim Ali Hamid, one of the leaders of the group, told a local radio: "We will carry out more attacks if Playboy refuses to stop publishing."
Playboy's Indonesian edition hit the newsstands last Friday for the first time and was quickly sold out.
The first edition of the magazine
quickly sold out
Copies later changed hands at more than three times the cover price of 39,000 rupiah ($4.33).
The magazine featured pictures of underwear-clad women, but also carried an interview with Pramoedya Ananta Toer, Indonesia's most famous author.
FPI activists, notorious for attacking Jakarta nightspots during anti-vice raids, have said Playboy is synonymous with pornography and is not fit for publication in the world's most populous Muslim country.
Earlier this year when plans for Playboy's debut were announced, Muslim leaders had expressed worries that the magazine would corrupt a culture already inundated by Western influences.
Susilo Bambang Yudhoyono, the Indonesian president, weighed into the debate in February to question the magazine's benefit to the country.
Indonesia's Muslims make up about 85% of the population of 220 million.