JAKARTA (Reuters) - When Pakistan's army stormed an Islamabad mosque housing a radical Islamic school last month, it raised questions in Indonesia: Was the Southeast Asian nation's own network of Islamic schools a breeding ground for militancy?
Or were the pesantrens, as Islamic boarding schools are known in Indonesia, just centres for learning the Koran along with some math, computers, geography and English?
"Pesantrens are part of our identity, part of a long-standing Indonesian tradition," Religious Affairs Minister Muhammad Maftuh Basyuni told Reuters.
"They have different principles. They chose to withdraw from the mainstream way of life because they denounce anything Western, which they associate with the colonial powers they fought in the past."
Islamic boarding schools in Indonesia, the world's biggest Muslim nation, largely escaped the spotlight in the wake of the Sept. 11, 2001, attacks on the United States.
They only came under scrutiny after the 2002 Bali bombings when a hardline cleric from a high-profile pesantren was accused of being Jemaah Islamiah network's spiritual leader.
The controversial Muslim cleric, Abu Bakar Bashir, who co-founded a pesantren in the 1970s which the International Crisis Group dubbed the "Ivy League" of militants, was jailed for conspiracy over the Bali bombings, although was later cleared.
Critics blame pesantrens for encouraging fundamentalism in Indonesia, a country of 220 million people, 80 percent of whom are Muslim.
But the vast majority of the 14,000 pesantrens are moderate and venerated, having educated much of the nation's Muslim elite.
"Pesantrens teach true jihad in the right way. Maybe two percent of the pesantrens have a wrong perception of Islam," Sofwan Manaf, principal of the Darunnajah Islamic boarding school in Jakarta, told Reuters.
"Modern pesantrens have a curriculum mixed between Islamic and non-religious teaching."
While pesantren enrolment makes up a small portion of Indonesia's school population, numbers have grown fast in recent years, partly in line with greater attention to Islamic values.
More than three million students are registered in Indonesia's pesantrens, which also form the backbone of the 40-million member Nahdlatul Ulama, Indonesia's biggest moderate Muslim group that accounts for 12,000 of the registered pesantrens.
In large parts of Asia, free board and education sometimes lure poverty stricken families to send their children to Islamic schools, many of them in rural areas that often lack other affordable education.
In a typical Islamic boarding school, students follow a regimented programme from dawn to dusk with tough rules.
But in Indonesia, pesantren students often defy stereotypes.
Some years ago, a band of veiled girls from a moderate Islamic school welcomed a former U.S. ambassador with a rendition of rock anthem "Stairway to Heaven".
Some clerics such as the turban-clad but leather-jacketed Abdullah Gymnastiar, the head of a pesantren in Bandung, also don't fit the stereotype.
Gymnnastiar, a household name in Indonesia because of his relaxed and chatty sermons on Islam that strike a chord with ordinary people, is best known for his moderate tone, use of hi-technology and hobbies such as riding Harley Davidsons.
At the Darunajjah pesantren, a sprawling campus with computers and basketball courts at the end of a narrow road crammed with roadside stalls or warungs, students say they disagree with the Bali bombers.
"I agree with jihad, jihad to defend Islam, but not like what they did," said Achmad Syaefuddin, a 17-year-old graduating from Darunajjah.
In the past, criticism has focused on Jakarta's hands-off approach to a smattering of uncompromising boarding schools such as Bashir's al-Mukmin Islamic school and its militant alumni.
Two Muslim militants, Amrozi and and Mukhlas, who have been sentenced to death for the 2002 Bali nightclub bombings, studied at the Al-Mukmin Islamic school in Central Java.
As a key ally in the so-called U.S.-led "war on terror", Indonesian authorities say they monitor pesantrens, but not in an intrusive manner.
"As Vice President Jusuf Kalla once said, we have to monitor pesantrens, and we have done that since decades. But we are not doing it in 'Big Brother' style," said Basyuni.
"We provide guidance and give directions to pesantrens. We also gave a helping hand in educating the resources and developing the facilities of many pesantrens."
International aid agencies have begun funding pesantrens in a bid to make their curriculum more mainstream.
But analysts say many unregistered pesantrens remain outside the reach of these programmes and continue to spread their rigid interpretation of Islamic teachings.
Analysts also say the government cannot touch pesantrens for political reasons.
"The government is reluctant to greatly interfere in the matters of pesantrens, even in those accused of teaching radical Islam," Sri Yunanto, an expert on radical Islam, told Reuters.
"Clerics and pesantrens represent a massive voting power. Imagine what the voice of 1,000 clerics can do to your political career?