Pictures of chocolate bars packaged with condoms have been published in newspapers and circulated on social media in the world's most populous Muslim-majority country in recent days.
The Indonesian Council of Ulema's chairman Ma'ruf Amin said that the body was investigating the reports, adding that it was against the sale of condoms as they "provide opportunities for people to engage in pre-marital sex".
"The sale of condoms has led to prostitution and free sex," he told AFP.
"We have long rejected the condomisation of our society."
He added that if the reports were true, "it is very possible that we will issue a fatwa restricting the sale of condoms freely in this country".
Reports said that shops in Malang, on the main island of Java, were selling the condom-chocolate offerings, and authorities in other cities launched raids on stores in search of the items.
Muslim clerics across Indonesia have warned against celebrating Valentine's Day, which falls Saturday.
They regard it as a Western celebration that promotes sex, alcohol and drug use.
Around 90 percent of Indonesia's 250 million people are Muslim, but the vast majority practise a moderate form of the religion.
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