President Megawati Sukarnoputri opened a conference of Indonesia's largest Muslim organisation with a rare attack on the "narrow fanaticism" of more extremist Islamic groups.
"We want to show that Islam is a peaceful religion and is capable of creating prosperity in the world," she told the national congress of the Nahdlatul Ulama (NU), which claims a membership of 40 million.
"With that view we can help or save those groups which are small but often claim to represent the ummah (faithful) and impose their narrow views, which are actually harmful to religion and the nation," Megawati said.
"We can also broaden our religious horizons and shun narrow fanaticism ... and the view that differences are wrong."
Megawati also expressed concern about the ignorance of many Muslims and called on religious leaders to play a greater role in education.
"Many of our brothers and sisters are still in the dark, intellectually, economically, culturally and in other fields," she said.
Indonesia is the world's largest Muslim-populated nation but Islam is not the state religion and different faiths are widely accepted.
Hardline groups like the Front for the Defenders of Islam unnerved foreign residents and potential investors and tourists last year with threats to expel Americans and other foreigners over the US attacks in Afghanistan.
The front, which did not follow through on its threats, has also launched raids on bars and nightspots.
The Laskar Jihad Muslim militia sent thousands of fighters to aid Muslims in battling Christians in the Maluku islands and around Poso in Central Sulawesi.
NU and the second largest Islamic organisation Muhammadiyah are traditionally moderate in outlook.
On Wednesday senior NU and Muhammadiyah officials and Christian church leaders agreed to oppose proposals by radical groups who want the constitution changed to require Muslims to obey Sharia Islamic law.
Cardinal Julius Darmaatmadja, chairman of the Indonesian Bishops' conference, said that for the sake of religious harmony Islamic law should not be recognised in the constitution, according to the Koran Tempo daily.
Darmaatmadja, as quoted by the Jakarta Post, said promoting personal interests above national interests would only pave the way for Indonesia's disintegration.
"Once we fail to respect other people's rights, our country will break up."
Muhammadiyah chairman Ahmad Syafii Maarif said the commitment to oppose the constitutional change may not be popular with many Muslims.
"I believe that many people within our (NU and Muhammadiyah) community will condemn our stance but I have warned them that we must be committed to promoting unity, which our founding fathers declared when establishing this nation," the Post quoted him as saying.
The issue will be discussed at the four-day NU congress, which is attended by 700 Indonesian delegates and representatives from Malaysia, Egypt, Sudan and Saudi Arabia.
Organisers said other topics would be Indonesia's foreign debt, corruption, terrorism and suicide bombings by Palestinians.