The report said some Christian communities particularly feared for their safety.
“There’s almost a sense that they are second-class citizens in their own country,” said Benedict Rogers, the organization’s East Asia team leader.
In response to the fall of Mr. Basuki, who used to attend Sunday Mass at St. Paul’s, Indonesia’s president, Joko Widodo, one of his key political allies, established a special task force to reinforce the country’s state ideology, known as Pancasila, which enshrines pluralism.
Despite Mr. Basuki’s case, violent attacks on religious minorities have decreased substantially in the past five years. The Setara Institute for Democracy and Peace, a nongovernmental organization in Jakarta, had recorded only 93 such attacks this year through August, compared with 264 in all of 2012.
“But the number of blasphemy cases because of social media, because people have comments on Facebook and groups report them to the police, that is growing now,” said Bonar Tigor Naipospos, vice chairman of the Setara Institute’s executive board.
Mr. Nur and Mr. Pitoy both said Indonesia’s core problem with religion is not intolerance, but a lack of education and understanding among its people. Less than half of all Indonesians have completed primary school, according to the government’s statistical bureau.
“Indonesia is Muslim-majority — you have to accept it — but the lower class has a very simple knowledge” of Islam, Mr. Nur said. “That is why, if you want to know about the essence of Islam, which is peace and tolerance, study the Quran.”
When asked if he thought that religious intolerance was growing in Indonesia, Mr. Pitoy, the pastor at St. Paul’s, said, “I don’t think so.”
“The problems are about poverty and making social justice a reality,” he said of the challenges facing the church. “Also, with globalization, there are failures internally, and it has created many sudden changes. It’s very important to have a common foundation, and we have it with our Constitution and Pancasila.”