"I reject jihad if it means to collect thousands of people to gather around and cry out expressions of hate to take revenge," said Umar Shihah, co-chairman of the Indonesian Ulemas Council, the country's top official Muslim body.
"But if jihad is to fight against provocateurs, it is allowed," he added, according to a report from Jakarta by Reuters.
Clashes between Christians and Muslims in the region have resulted in some 1,500 deaths over the past year, according to official estimates, and the government has been unable to stop the feuding.
Although the term jihad is often translated as "holy war," it can also mean striving hard to protect those who are suffering. Some Muslim militants have blamed the violence on the Christian provocateurs, and in the past week there has been a series of demonstrations in Jakarta urging a "jihad."
On Tuesday, however, President Abdurrahman Wahid, who is also a Muslim scholar, rejected calls for a holy war outright, saying they were likely to inflame the situation.
Meanwhile, the Geneva-based World Council of Churches, in a letter to Wahid, said that despite the deployment of security forces to put down the violence, the situation in the Moluccas has deteriorated over the past several weeks.
"The burning of the Silo church in Ambon a day after Christmas came as a rude shock not only to the Christians in Indonesia but also to the people at large," said the letter, signed by George Lemopoulos, acting general secretary of the international ecumenical agency.
The letter said that while it believes Wahid and other government leaders sincerely wanted to end the strife, "some leaders of the security forces are either responsible for or have directly committed grave abuses of human rights in the past, adversely affecting the credibility of these (security) forces."
It said that the government should act against those committing human rights abuses and try them for the crimes they have allegedly committed.
"To allow impunity for official actors to continue will tarnish the image of the Indonesian government in the eyes of the international community," the WCC said.