Hasyim Muzadi, chairman of the Nahdlatul Ulama said on Thursday most of the country's Muslims are moderates.
"What is being written in the newspapers are only the radical actions and it seems that actions that are not radical do not meet the (public) taste," Muzadi was quoted as saying by the state Antara news agency.
"Media reports did not reflect the truth in Indonesia where there are a lot of Muslims who act moderately and well," the head of the Nahdlatul Ulama, which claims 40 million members, added.
Indonesia is the world's largest Muslim-populated nation.
Muzadi said radical Muslims could be "counted with the fingers" and religious radicalism can exist anywhere in the world.
Many observers agree the Bali bombings last October tarnished the country's image.
More than 200 people were killed in the explosions that ripped through the heart of Bali's tourist centre.
The authorities blamed the Jemaah Islamiyah - which Indonesian police say is now headquartered in the country.
Dozens of its members have been arrested.
The US and other countries have linked the group with the al-Qaeda network of Osama bin Laden and has accused the Jamaah Islamiya of seeking to establish an Islamic state across much of Southeast Asia.