The warning from Bishop Humphrey Peters came one day after the Disasters Emergency Committee (DEC), an alliance of aid agencies including World Vision and Christian Aid, launched a major appeal for donations to help victims of the floods.
At least 1,600 people have died in the floods, while millions more are in need of aid. Bishop Peters said many Christians had lost everything.
“Our Christians, who are already deprived and marginalised, are in pathetic conditions. They have lost almost everything in their houses; they could only save their lives,” he said.
"Soon after the emergency phase that might last for a couple of months, the most important will be the rehabilitation.
“We are sure that some countries will come forward with aid packages, but hardly anything will reach the minority Christians. Do keep us in your special prayers."
Yunis Lal Din, leader of the Fellowship of Brethren Churches in Pakistan, told Barnabas Fund that many Christian families were facing a “desperate” situation after losing their homes and possessions.
“Many Christians were already in poor circumstances and are now doubly affected and do not know where to find help. It is great to know that brothers and sisters care so much in this time of national crisis. Thank you,” she said.
Christians make up less than 3 per cent of the population in majority-Muslim Pakistan and are often excluded from anything more than menial employment, meaning that the majority of them live in extreme poverty.
Barnabas Fund said islamisation was already gaining strength in Pakistan, where sharia law has been partially implemented, and that Christians were “likely to be neglected” where general aid is distributed.
Last year saw a sharp increase in the number of attacks on Christians in Pakistan, many under the pretext of blasphemy – a crime punishable by death. Rights groups are calling on Pakistan to repeal its controversial blasphemy laws, warning that they are being misused by extremists to settle personal vendettas with Christians.
Dr Patrick Sookhdeo, International Director of Barnabas Fund, said: "We greatly welcome the appeal by the DEC to help those affected by the devastating flooding in Pakistan but we would urge Christians to particularly bear in mind their marginalised brothers and sisters when considering their own giving.
“Barnabas Fund channels money exclusively from Christians through Christians to Christians who desperately need our help.
"They urgently need our assistance now and, looking to the future, will require long-term help to rebuild their homes and shattered lives."
Pakistani Christians living in Britain have called on the British church to give financially to Christians in Pakistan working to bring relief to survivors.
Vice-Chairman of the British Pakistani Christian Association, Wilson Chowdhry, said: “We are asking brothers and sisters up and down the country to pray for a speedy restoration of the homes and livelihoods of the affected local people.”