The cartoon row sparked anger throughout the Islamic world
Teguh Santosa, online editor of Rakyat Merdeka, is charged with inciting hatred towards a religious group.
Mr Santosa posted the cartoons in February at the height of international controversy over drawings which first appeared in a Danish newspaper.
The images, including one which showed Muhammad with a bomb in his turban, sparked anger across the Islamic world.
Islamic tradition explicitly prohibits any depiction of Allah and the Prophet.
Denmark was forced to temporarily close its embassy in the Indonesian capital, Jakarta, as days of protests peaked.
Mr Santosa said he published the images to give readers the full story on the cartoons issue.
"We just wanted to let people know about the cartoons, which were being strongly protested at that time," he told the Associated Press news agency.
Mr Santos, who was formally arrested and charged on Thursday, faces up to five years imprisonment if found guilty, his lawyer said.Media freedom watchdog Reporters without Borders condemned his arrest and called for the charges to be withdrawn.
Moderate, Tolerant Indonesia, som Robert Spencer skriver. Det må vist være kommentar nok.