The government had given the tobacco industry 18 months to comply with the 2012 regulation on tobacco control, which demands pictures or graphics on packs to warn about the hazards of smoking in addition to written warnings.
A government survey last year showed that 36 percent of the population aged above 15 smoke, with average consumption of 12 cigarettes a day.
"The aim is to provide the community with honest and accurate information in the form of pictures so they can decide (whether or not to smoke)," Health Minister Nafsiah Mboi told reporters.
An anti-tobacco group however said compliance has been low so far.
The National Commission on Tobacco Control said only six out of more than 3,800 cigarette products have the graphic warnings displayed.
"The government should enforce the law, there should be no tolerance even for the richest businessmen who violated the law," commission member Hakim Sorimuda Pohan told AFP.
Some of the richest businessmen in Southeast Asia's biggest economy are owners of tobacco firms.
Indonesia has not ratified the framework convention on tobacco control.
A pack of cigarettes in Indonesia costs much less than in many other countries, at a little more than $1.