They thought seeking refuge in the local church would save them from violence that has engulfed South Sudan.
But despite the usual sanctity of a church, St Andrew’s in Bor, Jonglei state, has become the scene of a massacre that took the lives of at least 14 female staff.
All churches played a significant role in unifying South Sudan during five decades fighting a civil war with Sudan until peace was brokered and independence came in July 2011.
Once again the church has been thrust onto the front line by providing much needed care for thousands now caught up in the internal conflict.
A fragile ceasefire keeps tensions high and church officials are increasingly at risk in a crisis described by a top U.N. official as a 'humanitarian disaster' with atrocities committed by both sides.
On Friday the Anglican church’s top cleric, Archbishop of Canterbury Justin Welby, visited St Andrew's that was not spared from fighting between rebels and pro-government forces.
Welby, who stressed the need for forgiveness, peace and reconciliation, said the killing of church leaders and attacks on church grounds was 'obviously a very, very major concern.'
'It breaks a long tradition of protecting those who are seeking to do good,' he said.
'I’ve heard particularly bad news of attacks on Christian people working as Christians in hospitals and that is a great concern.'
South Sudan's Episcopal Archbishop Daniel Deng Bul said what happened in Bor was a 'terrible crime.'
'They were all clergy,' he said. 'They wall worked at the church, did different jobs, bible readings and one was also an ordained pastor.'
Skye Wheeler, from Human Rights Watch, travelled to Bor and saw 'horrendous crimes had been committed.'
'In the church compound, eleven women had been killed, one with an obvious bullet hole in her head,' she said.
'In one of the rooms in the church compound I saw six women lying dead, this is very serious.'
It was not just St Andrews that came under attack in fighting that started mid December in Juba before spreading across the country, forcing 700,000 to flee their homes and costing many thousands of lives.
What started as a political struggle quickly within the ruling SPLM party turned to take on ethnic dimensions between the Dinka tribe loyal to President Kiir and supporters of Riek Machar, the former vice president, a Nuer.
Now more than 79,000 people have taken refuge in United Nations bases while tens of thousands have sought shelter in church compounds, in conditions described as "unbelievably dire".
St Joseph’s catholic church in Malakal, Upper Nile state, has become home for 9000 mostly Shilluk tribesmen and women who are forced to live in overcrowded conditions with little access to water or sanitation.
Antony Achuil Arop, a worker with the church, said leaders came under regular attack, were robbed and often receive death threats.
'The Bishop’s car was stolen, they took all the things,' he said.
'I was threatened many times. A soldier wanted to shoot me, said I was keeping the enemy. But last time he was the one who ran in here when chased away by the rebels.'
'We are neutral, but they get drunk and come back and are angry. I say 'you want to kill me? Last time I was the one who saved your life,'' he said.
Cardinal Gabriel Zubier Wako, President of Sudan Catholic Bishops Conference, said the Diocese of Malakal, which covers Jonglei, Upper Nile and Unity states, will receive extra support.
'It is the role of Christian leaders, speaking as the voice of voiceless communities, to call for a resolution to the political and humanitarian crises,' he said.
'Churches are places of refuge for people who have felt threatened or are running for their lives. But there have also been hostile groups that have thought they’d find easy targets there.
'People have gone in and are trying to kill people or are dragging them out. It is unacceptable.'
Watch SBS report on South Sudan 30/01/14: