Christians and members of other minority religions are being treated as second-class citizens, said Father Mario Rodrigues, the Lahore-based director of Catholic Mission. "They often receive little assistance or are excluded altogether," he told Fides, the Vatican's news agency.
Aid is being delivered by "government officials sympathetic to Islamic fundamentalism or by Muslim relief organisations", Fides claimed in its report, citing other unnamed aid workers.
About 200,000 Christians in Punjab province and about 600,000 Christians and Hindus in Sindh province have been affected by weeks of monsoon rain.
At least 1,600 people have been killed in the country's worst natural disaster, and on Friday, officials warned that the death toll was expected to rise significantly as many people remained missing.
Over the past two days, fresh floods from the surging river Indus smashed through levees in two places, forcing one million people from their homes.
Ahmad Kamal, spokesman for the National Disaster Management Authority, denied the accusations of prejudice.
"We have no discrimination, no requirements, no checklist. Aid goes to everyone," he said.
However, Nazir Bhatti, President of the Pakistan Christian Congress, urged donors to make special provisions for Christians.
"I appeal to organisations and countries which are giving aid to government of Pakistan for flood victims to allocate separate or special funds for Christian flood victims and transfer it to Caritas Pakistan or Bishops Conference of Pakistan for food, tents and medical facilities," he said in a statement.
In all, some eight million people need emergency help and the monsoon season is due to last another three weeks.
SIC: TCUK