"The percentage of dirty water not fit for human consumption could lead to diseases more dangerous than cholera, such as some kinds of life-threatening hepatitis and diarrhoea," the ministry said in a statement on 22 October.
It said the survey results were based on laboratory tests by its Nutrition Research Institute in Baghdad and health laboratories in the provinces, and covered the period 1-15 October.
"Theoretically, there are a lot of areas in Baghdad with drinking water networks but either the quantity is insufficient, or the added chlorine is ineffective because of leaks which allow water to mix with sewage," the statement said.
The ministry called for immediate government action to ensure adequate supplies of clean drinking water to all residents.
The country is currently grappling with an outbreak of cholera which has left eight people dead.
Health Minister Salih al-Hasnawi on 22 October defended the procedures adopted to combat the disease and put the number of laboratory confirmed cases at 534 nationwide.
"We immediately set up a committee to monitor the outbreak, and we have conducted field visits to check on chlorine levels in drinking water, and distributed 50 million of water treatment tablets," al-Hasnawi told parliament.
Cholera is a gastro-intestinal disease typically spread by contaminated water. It can cause severe diarrhoea, which in extreme cases can lead to fatal dehydration. Treating drinking water with chlorine and improving hygiene conditions can prevent the disease.
The Health Ministry and the World Health Organization have blamed the country's rundown water and sanitation infrastructure for the outbreak.
Lack of security, corruption, neglect and insurgent attacks have left Iraq's public services in tatters. Limited electricity, a shortage of safe drinking water and rundown sanitation and sewage systems are causing diseases and frustration.
Water treatment plant
Hazim Ibrahim, deputy head of Baghdad's water directorate, said the government had earlier this month approved a project to build a huge water treatment plant in Rasafa, eastern Baghdad.
Ibrahim said the project was valued at about US$1 billion and was designed initially to supply 910,000 cubic metres (cu. m.) of water, with an eventual planned capacity of 2.275 million cu. m.
He said the daily demand for drinking water in Baghdad was at least 3.25 million cu. m., though the amount piped daily was only about two million cu. m.
"Our water pipelines are over 30 years old and that is the main reason for contamination as the water gets mixed with either sewage or underground water," he told IRIN.