Christian Solidarity Worldwide (CSW) is asking President Obama to have an honest conversation with President Joko Widodo about conflicts in the country during their meeting this weekend.
Earlier in the week a Protestant Christian Church of Pakpak Dairi (GKPPD) church and a chapel, Undung-undung Katolik Desa Mandumpang, were destroyed by the government in Aceh Singkil.
It has also been reported that at the beginning of the month one man was killed and a church was burnt down during religious clashes.
Violence is thought to have broken out after it was agreed that around 13 local churches would be demolished because they are thought to have been built without permission.
Catholics and Protestants have both returned to their homes however it is still unclear who is behind the attack.
CSW says attacks like this represent a disregard for religious minorities due to the government's lack of action to find and bring to justice those responsible.
It has published a special report on Indonesia that details the government's reluctance to act following instances of religious intolerance and violence.
Key recommendations in the document include the reform or repeal of laws governing the construction of houses of worship, which discriminate against religious minorities, and to revise the curriculum for religious education.
CSW's Chief Executive Mervyn Thomas said: "Indonesia's tradition of religious pluralism and tolerance has been challenged in recent years and CSW urges President Obama to raise the plight of the country's religious minorities with President Joko Widodo when he visits the US.
"We continue to call on President Widodo to ensure the repeal of discriminatory legislation that affects religious minorities and to ensure that violations of religious freedom are properly investigated and the perpetrators are brought to justice."
