'Some lay down. Others begged for mercy. They did not listen'

Soon after the bombing of Afghanistan began, menacing slogans were daubed on walls near St Dominic's Church in Bahawalpur. Police dispatched officers to stand guard outside. Yestrerday, it was the Muslim policeman, Mohammad Salim, who was the first one to die.

It was 8.55am, and the service inside St Dominic's in the southern Pakistani town was drawing to a close. Constable Salim would have seen the motorbikes pull up, and the men – five or six, depending on the witness – who climbed off, carrying long heavy bags.

The men were bearded, conventionally dressed in loose cotton shirts, and unmasked. Mr Salim might not have realised anything was wrong until the bags were unzipped and Kalashnikov assault rifles were pulled out. By then, it was too late for him, and for the people praying inside St Dominic's.

One of the gunmen waited at the gate by Mr Salim's dead body, and another lingered in the grounds. Three walked into the church which contained a congregation of some 60 people. The Kalashnikovs were on automatic; the firing went on for about five minutes. Those inside could hide under the wooden pews. They could run behind the altar, and try to shelter their children from the bullets. Otherwise, they were defenceless. Last night, there were 16 bodies in the church and reports that more had died in hospital.

The first to die was the priest, Pastor Emmanuel. Five of the dead were children, including two brothers of two and eight years old. Four were women, and half a dozen of them were members of the same family. A man named Shamoon Masih received bullets in the leg and the arm. "They had no mercy for the children," he said. "They had no mercy for the women. They could see that small children were being hit by bullets, but they kept firing."

Ali Shah was lucky enough to be sitting in the front pew when the killers appeared, as far away from them as could be. "Some of [the congregation] lay down," he said. "Some begged for mercy. They didn't listen." Less than 10 minutes after the motorbikes had first pulled up, it was all over.

Sister Anna Bakhshi, a nun at St Dominic's Covent next door heard the shooting, watched the men run out of the compound, and ran into the church herself, seconds after they had gone. "I saw dead bodies," she said. "There wasn't a single wall that didn't have a bullet hole. There were holes in the walls, in the floor, in the altar. The people were hysterical, they were calling out the names of the people who were dead. There was blood ...

"The convent is right next to the church so we heard all the noise of the firing. This wasn't just one gun firing – there were three or four of them and they were all firing on automatic all at the same time. Since 11 September, we knew that something might happen. For Christians in this country, it's an automatic reaction – you feel afraid. But never this, nothing like this."

Pakistan has always been a violent and troubled country, and murders, gang killings, and sectarian assassinations occur almost daily. But even by local standards, this was a vicious and incendiary attack – the worst domestic act of terror in Pakistan since the bombing began. "It is a security failure," said S.K. Tressler, the Christian minister for minorities affairs. "[The local authorities] should have properly reacted to these threats."

The President, General Pervez Musharraf, said in a statement: "The method used and the inhuman tactics clearly indicate involvement of trained terrorists. I would ... like to assure everyone that we will track down the culprits and bring them to justice."

Ominously, in another mysterious attack, three people were killed in the south-western city of Quetta when a bomb exploded on a bus.

By yesterday evening no one had claimed responsibility for either attack, but even if they did not know their exact identitities, no one in Bahawalpur has any doubt about the killers' affiliation. One witness reported that they shouted "Pakistan and Afghanistan, graveyard of Christians", "Allah is great", and "This is just the start".

Sister Anna doubts that version of events, "but there's no question that this was because of the attacks on Afghanistan.

"Most of the Muslims are our friends," she said. "The Muslims who live round here, they are as shocked as we are, they are grieving. But there are extremists, organisations who believe that as non-Muslims we're part of the UK or the US. They call us infidels. We're not part of the community."

Does the St Dominic's massacre mark the beginning of what has long been predicted – a violent backlash against those symbolically associated with the United States, Britain and the West?

On 7 October, three hours before the bombing raids began, I sat in a hotel in Karachi with Shafiqur Rehman, spokesman for Defenders of the Holy Prophet, one of the most extreme of the country's militant groups. "If there is any attack on Afghanistan," he said, "there will be a religious war, and we will threaten American lives and property." But so far, within Pakistan, these threats have been unfulfilled.

There have been vociferous demonstrations in many parts of the country. In the North-West Frontier Province and in Quetta, there have been a handful of deaths, when police and demonstrators have fired on one another. But the rhetorical fire and brimstone, the chants of "Death to America", and the incineration in effigy of George Bush and Tony Blair, had not – until yesterday – been matched by acts of terror.

All over Pakistan, the obvious foreign targets – embassies, consulates and big companies – have been encircled with barbed wire, armoured personnel carriers and rifle-carrying police. Many ex-patriates have sent their families home. Even in the sedate modern capital, Islamabad, machine guns peep out every few hundred yards from behind nests of sandbags. So perhaps it was inevitable that the backlash would begin with one of the most vulnerable communities – Pakistani Christians.

Nationwide, Muslims represent 98 per cent and Christians just 1 per cent of Pakistan's population of 150 million, half of them Protestant and half of them Catholic. St Dominic's is a Roman church, but every Sunday a congregation of Protestants, lacking premises of their own, hold their service there.

"The church was almost empty when it happened, but a few minutes later, the Catholic service would have started, and there would have been 400 or 500 people in there," said Sister Anna. "I think they mistook the time. I think they wanted to kill many more."

Vague threats began soon after the start of the bombing campaign, according to Sister Anna. "Sometimes people make remarks in the street," she said, "and there were slogans on the walls – 'The Americans and British are infidels', 'Kill all infidels no matter where you find them'."

On 8 October, as principal of St Dominic's School, she wrote to the authorities requesting more protection. What she feared was verbal abuse, jeering or jostling of the children, perhaps the odd thrown stone. "We were afraid, it is true," she said. "But this ..."

Today the bodies will be removed from the church, and buried. The pews and aisle will, be washed of blood, and the school will be closed for who knows how long.

"The community is very fearful and very angry," said Sister Anna. "What will happen next? And will this start to happen in other churches all over Pakistan?"