Religious intolerance must be high on the agenda during President Obama's meetings with Indonesia's President Joko Widodo this week, a religious freedom charity has said.

Christian Solidarity Worldwide pointed to several recent examples of religious persecution in Indonesia, whose population is 87 per cent Islamic.

Several churches have been subject to arson attacks over the last few weeks in the the conservative province of Aceh, whose regional government has imposed sharia law. The local government in Aceh also agreed to demands by extremists to demolish at least 13 churches that were believed to have been built illegally.

"These events illustrate the trends of religious intolerance and impunity for the perpetrators of attacks on religious minorities in Indonesia," a statement from CSW read.

The US State Department's report on international religious freedom released this month pointed out that although the constitution is secular and guarentees freedom of religion, certain laws and practices restrict religious freedom.

"Instances of abuse and government inaction occurred, especially against members of minority religious groups," the report notes.

"There were instances where local governments and police gave in to the demands of intolerant groups to close houses of worship or otherwise restrict the rights of minority religious groups, and there were reports of local officials abetting intolerant groups."

"Certain local governments imposed aspects of sharia on non-Muslims," the report added, referring to the Aceh province.

CSW's chief executive said that that Widodo's visit provided a good opportunity to raise the issue of religious freedom with the president.

"Indonesia's tradition of religious pluralism and tolerance has been challenged in recent years," said Mervyn Thomas. "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."