To the East Timorese children of a catholic school in Suai, on the island’s south coast, the Indonesian flag-raising ceremony that marks the beginning of each school day is one to be endured rather than savored.

Yet to watch the precision of the children’s movement as they unfurl the flag, and to listen to the thunderous clap of 126 students pulling their saluting hand to their hip as the red and white flag reaches its zenith, it is easy to mistake their discipline as devotion to the government that has ruled this land since 1975.

Nothing could be further from the truth. "They just do it," a nun tells me. "They have to. We all have to."

It is a truth reinforced by the grim statistic that of the 126 students, 36 of them are orphans – -made so by the soldiers in East Timor representing the flag they now salute. It is a statistic mimicked all over the province – in whatever schools one chooses to wander into. It is also the reason that the trouble in East Timor is far from over. Time and time again these people of simple life and faith will tell you that the fight is no longer just in the mountains, where the dwindling numbers of Falintil soldiers continue to resist, but it has now swept down to the cities, the towns, the villages, places where people can congregate and discuss in secret the occupation that has affected each one personally.

"We continue to fight, but not with guns," one man told me. "It may appear that we have accepted the Indonesians, but that is only because to do otherwise would mean prison or death. But we continue to fight with our heart and our minds."

Most people met have a story to tell of the tragedy that is Timor: the gay housekeeper who had his testicles crushed between two bricks; the cab driver whose pregnant mother was raped by soldiers while he as a young boy of 12 was forced to watch; the teenage simpleton, but not always so, who showed me the mark of a branding iron on his leg, the burn marks of electrocution on his hands, and the holes in his head where he was beaten, just a fraction too many times, by a piece of wood punctured with nails; and the Suai schoolgirl who has not seen her parents since they were arrested in January 1997 during a celebration marking Bishop Belo’s winning of the Nobel Peace Prize.

Interestingly, to many of the soldiers based in East Timor, most of whom were not even born when the Indonesians first invaded in 1975, the purpose of their mission is perceived to be in the best interests of the people: "We are fighting the communists. If we were not here many of these people would be killed by the guerillas." one told me, with not a hint of irony.

He was a member of a special police unit, an elite group of commandos from Sumatra brought to East Timor to rid the country of Falintil once and for all. His unit’s soldiers were all trained in four disciplines: scuba, explosives, hand-to-hand combat and radar. It is the last two that have bought him and his unit to Timor. The Indonesian army, ABRI, are now using sophisticated aerial surveillance technology to detect movement on the ground, then dropping commandos in to surprise the poorly-nourished, poorly-armed fighters.

The soldier bragged that the "skin" of each East Timorese fighter brings him a bonus from his government of 500,000 rupiah; a story confirmed by two other soldiers elsewhere in East Timor.

But the estimated 250 guerillas left in the hills are now merely a symbol of the continuing East Timorese struggle. The real fight is taking place in the cities, like Dili, where Falintil members do not wear combat fatigue or carry guns.

Most are East Timorese men educated by the Indonesians, who during the day work as civil servants for the government and at night meet clandestinely to organise the resistance.

"Our greatest challenge is to counter the propaganda put out by the Indonesians," said one of the leaders in the central command of Falintil.

"We have a mission to politicize the community here, so they know about the reality. We now have an underground magazine called Tuba – which means to resist – where the objective is to distribute information to everybody, even sometimes to the government people. We have to give them information so they know the reality – the reality of the number of people imprisoned, tortured, and killed."

The measure of the East Timorese urban resistance can be taken by the continued buildup of Indonesian troops.

In Dili, the capital with a population of 176,000 people, there are now 15,000 soldiers. In East Timor, a province with a population of 800,000 people, the number is estimated to be 30,000. And the killing never seems to stop, on both sides.

Add to that the estimated 200,000 people who have been slaughtered since the Indonesians arrived, and it is easy to understand why the most prominent landmarks in East Timor are cemeteries.