The apology published on the front page of the English newspaper The Jakarta Post stated that the caricature on page 7 of the July 3, 2014, edition had insulted religious symbols.
The daily expressed its deep regret over the mistake of judgment, which was not intentionally meant to slander or disrespect a religion.
The daily stated that the caricature was aimed at criticizing the use of religious symbols in general, especially in the flag of ISIS (the Islamic State of Iraq and Syria) that has committed violence even on fellow Muslims.
The caricature had also condemned the ISIS that has threatened to attack the Kabah in Mecca as one of its agenda.
Earlier, the Indonesian people had been shocked by the publication of the caricature, which has been considered offending to Muslims.
The chairman of the Indonesian Council of Ulema, Amidhan, said here on Tuesday that he had seen the caricature, and, according to him, it had hurt the sentiments of Islam and Muslims.
He however appealed to Muslims in the country not to be provoked.
"Their disappointment had better be channeled through legal means, the Press Council, or a criminal lawsuit," he said.
One of Indonesias largest Islamic organizations meanwhile had called on Indonesian Muslims not to be provoked by political conflicts in other countries.
"Muslims in Indonesia need not be offended and over-react emotionally because of the recent publication of a caricature criticizing Islamic State in Iraq and Syria (ISIS)s activities in Iraq and Syria. Do not belittle Islam by considering the caricature of ISIS an insult to Islam," the secretary of Muhammadiyahs executive board, Abdul Muthi, said.
He noted that Indonesian Muslims must not be co-opted by other countries political problems.
He said ISIS is only an Islamic movement organization involved in politics in other countries.
"The caricature meanwhile is more political than religious and is not related with politics in Indonesia. I believe The Jakarta Post did not mean to insult and hurt Islam," he said.
However, to anyone who feels offended by it, he suggested that the person bring the case to the Press Council or report it to the police.
Editor: Ella Syafputri
Copyright © ANTARA 2014