Jessie Wright, Dili – Buried deep in a neighbourhood of tin-roofed shacks, between a Christian church and an English-language school, sits one of the few mosques in East Timor.

The morning sun sparkles from the copper dome and the crescent mounted on top. Schoolgirls in headscarves walk in twos and threes through the gates. In the shadow of the mosque, boys kick a small ball back and forth.

These children are part of what is left of a religion so popular that in the 1980s and 1990s all 13 districts in the country had at least one mosque, sometimes more. Back then a Muslim in East Timor usually meant being Indonesian or supporting Indonesia, but after waves of violence rocked the country following independence in 1999, many Muslims fled for good.

The 27-year-old Masjid Annur mosque serves more internationals than locals these days and provides shelter for a few dozen refugees. But the building is falling apart. Inside window panes are broken, ceiling tiles are rotten, floor tiles are cracked and broken, and dirt covers everything. Yet for a faithful handful of East Timorese, the mosque is a school, a home, a place of worship and a place of refuge.

Jose Angelo Srifulloh, the mosque's co-ordinator, said he was born a Catholic in a border district far from Dili but became a Muslim when he was 26.

"I went to school in Java for eight years to study religion," he said. "That's when I became a Muslim." He said Islam made more sense to him than Catholicism. Most people in East Timor would disagree with this, but the differences do not spark conflict.

"Religion is each person's responsibility," Mr Srifulloh, 49, said. "We can't say what anyone else can believe. It's up to the individual person."

For 24 years this former Portuguese colony fought for independence against Indonesia, and in 1999 East Timor won. Since then South East Asia's poorest country has been trying to define itself politically and socially – something not quite Portuguese and not quite Indonesian. Portugal ruled the country for 500 years, so its no surprise that 98 per cent of East Timorese consider themselves Catholic.

Though the country shares its western border with Indonesia, East Timor remained isolated from Islam until the 1975 Indonesian invasion. But the invaders had little interest in forced conversion, and even after 24 years Timor is still less than one per cent Muslim.

During the civil unrest in 2006, which led to dozens of deaths in Dili and left more than 100,000 homeless, the mosque was not touched, even though dozens of nearby shacks were burned to the ground.

Mr Srifulloh said East Timor should be proud of its religious tolerance. "We're all East Timorese," he said. "We want to show an example to the world that there is no real difference between Catholics and Muslims."

There is something about East Timor not usually noted by the authorities – nearly everyone follows traditional beliefs that include being linked by clan to a spirit house kept on ancestral land.

Dewi Ratna Sari, 15, lives in the girls' dormitory next to the mosque. Her father is Indonesian and mother East Timorese, and both are Muslim. Ms Sari was raised Muslim and moved to Dili last year to attend high school at the mosque. But ties to her clan's spirit house are strong.

"The culture of Timor is based on the uma adat [spirit house]," she said. "You have to go and talk to the elders and listen to what they say. We all go, though we can't eat pig or dog or anything because we're Muslim and that's forbidden by Muslim law."

Mr Srifulloh is more circumspect. Although he admits he has a sacred house in his home district, he said he does not go to any traditional ceremonies.

"Each of us must analyse what is sacred," he said. "Why did our grandfathers consider this stuff to be sacred? We cannot simply accept a thing's holiness just because our grandfathers worshipped it. If it doesn't contradict Islamic law, OK, we can accept it."

However, he still believes in the adat system – but only as a Muslim. "I don't go to the ceremonies, but I do believe in it," Mr Srifulloh said. "But I've thought about it based on my religious education in Islam."

For centuries, Catholicism in East Timor has had to exist alongside the adat system, and Islam is doing the same.

"If you are alive you have to have an uma adat," Dewi Sari said. "If you don't have one, you'll never have a good life. Your grandfathers gave life to you and so you must respect your grandfathers."

"There are a lot of similarities between Islam and traditional East Timorese beliefs," Mr Srifulloh said. "In Islam we are meant to go to Mecca and pray there because it's a sacred place. We have many sacred places in East Timor, too. In Islam the star and crescent are important symbols of our religion, and we see these symbols used in traditional East Timorese ceremonies as well."

In any case, Mr Srifulloh said, he was happy East Timor's brand of Islam is its own. "I always say, 'Islam is not Indonesian and it is not Arabian'," he said.