Some communities were still recovering from last summer's devastating floods when heavy monsoon rains deluged the country's Sindh Province in recent weeks, killing at least 248 people and destroyed around 665,000 homes.
There are grave concerns that the more than 200,000 people sheltering in emergency camps will fall victim to water-borne diseases. There are also reports of food shortages.
The Diocese of Hyderabad has been badly affected by the floods and is appealing for 4.4 million Pak Rupees (around £30,000) to assist 1,000 families in the area with food and health and hygiene kits.
ACT Alliance, whose members include Christian Aid, has launched an appeal for $1.7m (£1.1m) to provide shelter and household supplies to affected families in the south of the province.
According to the BBC, the vast flood waters are making it difficult for aid workers to reach the estimated 8 million people affected by the floods.
The launch of ACT Alliance's appeal comes as the umbrella organisation's leadership met senior officials in Punjab this week to build closer relations with officials.
ACT Alliance General Secretary John Nduna received assurances of the authorities' willingness to working with people of all faiths.
He said: "Although Christianity is the minority, the work ACT has been doing has been highly valued. It shouldn't hinder us in delivering aid."
Barnabas Fund launched an appeal last week to support Christians flood victims after receiving reports that they were being overlooked in the distribution of aid.
One church leader in Pakistan told the agency: "I am terribly sad to see the destruction and poor condition of the people affected by heavy rains.
"I have noticed and seen that Christians are being deprived of the help, relief and support that other people are getting."