According to the Pakistan Council for Research in Water Resources (PCRWR) report, bacterial contamination, a major cause of water-borne diseases, especially diarrhoea, was 65 percent in 2004, 40 percent in 2003 and 74 percent in 2002.
The report, which will be made public in about 10 days, is the result of a five-year survey that analysed quality and levels of contamination in the country's water supply, Dawn said Monday.
In Islamabad, 27 samples were taken for the survey - 19 from tube-wells, two from water supply sources, one from a water tank, one from a reservoir, one from a bore-well and three from taps in homes.
Out of the samples, only 26 percent proved safe for human consumption, while 74 percent tested positive for bacterial contamination.
According to the council, the cause for the contamination lay not at the source of the water supply - the Simli Dam - where proper chlorination is done to kill micro-organisms, but elsewhere.
"Broken water supply pipelines or leakages are the major causes," Dawn quoted council chairman Mohammad Akram Kahlown as saying.
"Islamabad's water supply is intermittent. And every time the supply is stopped negative pressure builds up that sucks in dirt and other material through these leakages or openings in the pipes. Micro-organisms gush into cistern systems or water tanks in houses every time the supply is resumed," Kahlown added.
While Islamabad suffers, the quality of water is much better in twin city Rawalpindi, where bacterial contamination was reduced to 53 percent in 2006, compared to 87 percent in 2002.
According to the expert, over 80 percent of the samples collected from different parts of the country in the past five years contained bacteria.
In cities like Bahawalpur, drawing water from taps was akin to taking it from a swamp, Kahlown maintained.
"It is simply (because of) mismanagement. A lot of water contamination problems can be solved if proper chlorination is done by the authorities," he added.
According to the report, bacterial contamination in Quetta has gone up to 71 percent in 2006 from 50 percent in 2002; in Hyderabad to 93 percent in 2006 from 73 percent in 2002; and in Gujranwala to 64 percent in 2006 from 29 percent in 2002.
In Ziarat in the North-West Frontier Province, where Pakistan founder Mohammad Ali Jinnah spent his last days, bacterial contamination was a staggering 100 percent from 2002 to 2006.