Thousands of people were caught up in the Glasgow alert
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Testing of Scotland's water supplies for the cryptosporidium parasite is to be increased at a cost of £2.8m a year.
Ministers have told Scottish Water to check every water treatment works for the organism at least once a month.
Cryptosporidium caused a health scare in Glasgow in 2002, when 160,000 people were forced to boil their water after high levels of the parasite were found.
Environment Minister Ross Finnie said the new measures would provide an early warning system.
Cryptosporidium contamination can lead to an illness which causes severe abdominal pains, vomiting and diarrhoea.
Health scares
The Glasgow alert was sparked by the discovery of the parasite in water from the Mugdock Reservoir in Milngavie, East Dunbartonshire.
Edinburgh and Aberdeen have also experienced similar health scares.
Ministers have now revised the cryptosporidium directions to Scottish Water.
The additional monitoring will come into effect from June, with the frequency of the testing being based on the risk in each area.
Mr Finnie said much had been done to reduce the risk of the parasite entering public water supplies.
"The availability of far more data on cryptosporidium will not alter current low levels of risk," he said.
"Increased monitoring will, however, provide invaluable information and early warning on those locations where the prevalence of this organism is highest."
Dr Colin Ramsay of the Scottish Centre for Infection and Environmental Health (SCIEH) said: "Increasing the amount of water testing will hopefully help to clarify the relationship between finding the cryptosporidium organism in water and the risk of becoming ill.
Tap water
"As a public health priority, NHS Boards and SCIEH will continue to carry out active surveillance of illness as part of this process."
Scottish Water's chief executive, Dr Jon Hargreaves, welcomed the announcement.
He said: "Since Scottish Water was created 20 months ago much has been done to improve the quality of our customers' tap water.
"These measures will further help to ensure the safety of the country's water supply."