Hundreds of kilometres of the Murray have been affected by algal blooms over the past month, and scientists have confirmed the intrusion of a strain of algae not usually found in the cooler waters of southern Australia.

Known as Cylindrospermopsis, the algae traditionally has grown in Queensland's tropical waterways. It was first discovered in 1985 after a spate of human poisonings at Palm Island.

It is potentially toxic to the liver and other organs of humans and animals - particularly after contact with raw, untreated river water - but it is not considered capable of surviving the water purification conducted for the drinking water supplies of Victoria's Murray towns.

Water quality in the Murray is monitored and tested by a joint committee of Victorian and New South Wales officials.

A spokeswoman for the committee said that while traditional cool water algal species were still dominant in the current bloom, an intrusion of cylindro had occurred.

''Small amounts of Cylindrospermopsis have been recorded in samples collected from several sites on the Murray River in mid-February 2010,'' she said.

''We have noticed that it has become more common in samples collected in the Murray River from the [Wodonga] Hume Reservoir to Swan Hill during mid-March 2010, when that water is warmer.''

A trace of Cylindrospermopsis was detected during a test of the Murray in 2000, and again during the blooms that hit at Easter last year.

But the strain appears to be advancing, with officials saying that about 3 per cent of the biomass of the current Murray River bloom was confirmed as being Cylindrospermopsis.

Australi an Conservation Foundation water expert Dr Arlene Buchan said it was time to ask if the arrival was an indicator of climate change.

''If you don't have enough flows coming through the river you will get increases in algal outbreaks, and if we are starting to see nasty ones that are likely to have come from tropical regions then the sooner we act the better,'' she said.

The Rudd government has purchased 800 billion litres of water entitlements across the Murray-Darling river system. The entitlements have enabled 79 billion litres of environmental water to be delivered to significant wetlands.