Numbering around 6 million, Shia Muslims form under 3% of Indonesia's population. Despite its history of tolerance and religious diversity, they have become the target of intimidation in recent years, even being driven out of villages by mobs of vigilantes.
Some Muslim organisations in the Sunni-dominated country have been calling for the government to impose restrictions on them, arguing the Shia Muslims are not practicing real Islam.
Last month, the Indonesian Ulema Forum (Forum Ulama Ummat Indonesia, FUUI) issued a fatwa demanding that the Ministry of Justice and Human Right and the Ministry of Religious Affairs revoke the licence of all organisations with a Shia viewpoint and ban their activities.
"We've been monitoring Shia groups in West Java for more than 20 years and they seem to be braver in practicing their belief openly. Shia is actually a form of blasphemy against Islam because they have different view on the leadership of Muslim people," FUUI leader Athian Ali Muhammad Da'i told Khabar Southeast Asia.
"Please don't get us wrong. We respect any religion. But if Shia people want to keep practicing their view, they must establish their own religion without Islam's name because Shia is not part of Islam," he said.
"It is just like our demand to [the minority sect] Ahmadiyah to establish their own religion if they want to practice their view," he added.
But not all Muslim leaders agree. According to Imdadun Rahmat, deputy secretary general of the moderate Islamic organisation Nahdlatul Ulama, Sunni and Shia Muslims have the same God, Allah; the same prophet, Mohammad; and the same holy book, the Qur'an.
"Even though Shias differ on who was to take over the leadership of the Muslim community after the Prophet died, we still consider Shia as part of Islam and we do not dismiss Shia," he said.
It is not the government's role to intervene in religions disputes or enforce fatwas, he added.
Religious organisations can issue fatwas or decrees on certain topics but they must not force any individual or government to implement them, Imdadun said.
"Fatwa is a study which is conducted by Islamic jurists (ahli fiqih Islam) on a certain topic," he went on to explain.
"In other words, a fatwa is a religious opinion that is issued by a religious organisation on any topic and it is not a legally binding instrument. It is implemented by an individual who has a belief in the fatwa," he said.
"Therefore, no one can be forced to implement a fatwa in his or her life. Or force the government to make it a foundation for public regulation."
A Shia cleric, Tajul Muluk, is currently on trial in Sampang, East Java for blasphemy. Muluk, the head of a Shia Muslim boarding school on Madura Island, was arrested after the Indonesian Ulema Council (MUI) issued a fatwa describing his teachings as "deviant".
According to a report in The Jakarta Globe, more than 300 members of Sampang's Shia community were displaced in December 2011 when a mob of 500 people attacked and burned Shia houses, a boarding school and a place of worship there.
The persecution of religious minorities has little precedent in Indonesian history, Rumadi, a senior researcher at the Wahid Institute, noted in an April 29th article in The Globe.
"One of our conclusions is that society has become prone to intolerance. What used to be considered as acceptable has become unacceptable," he said, citing mob violence against Shia Muslims in particular.
Abdullah Beik of Ahlul Bait Indonesia (ABI), an organisation that advocates for Shia Muslims, described FUUI's demand as odd.
"It needs to be understood that even in Saudi Arabia, Shia Muslim has a place and we can go there for Umrah. Therefore, the FUUI demand is very odd," he told Khabar.
Moreover, Abdullah added, we must not forget that since we live in Indonesia, which has a motto of Bhinneka Tunggal Ika (Unity in Diversity), we must respect each other and live side by side in harmony with other people who have different backgrounds.
Jakarta resident and Sunni Muslim Ahmad Aqiqi, 30, also does not agree with the FUUI edict.
"As long as their religious practice does not violate any human right and regulation, I think every Muslim has the right to choose what kind of Islam they want to believe," he said.