"We have sent an urgent appeal to all our dioceses and parishes requesting prayer," Sharoon told New Delhi-based Christian Today.
As a union of four major denominations, the Church of Pakistan comprises over eight dioceses and 400 parishes across the country.
In the Diocese of Peshawar, the church body has launched an emergency relief and rescue program for families affected by the flood.
The program is assisting more than 1,300 families, particularly Christians and other minorities. The diocese is also providing food for the victims.
So far, more than 1,500 people have died in Pakistan's worst flooding in 70 years.
The United Nations and several countries have announced millions of dollars in aid to help the flood victims in Pakistan.
The United Nations said clean drinking water and sanitation were urgently needed to stop disease spreading among survivors.
In response to the flood disaster in Pakistan, U.N. Secretary General Ban Ki-moon has asked his special envoy for assistance to Pakistan, Jean-Maurice Ripert, to travel to the country "as soon as possible."
International assistance, meanwhile, is being sought for victims of the disaster.