Five of the six top scientists in charge of monitoring the health of Sydney's water have had their positions axed as part of state government cuts experts warn will compromise the safety of drinking water.

The loss of top scientific expertise is part of deep staff cuts of up to 25 per cent in the agency created to ensure the safety of Sydney's water catchment after the city's drinking water crisis in 1998.

Four top scientists, including Penny Knight, the organisation's director of science, two senior scientists specialising in microbiology and catchment management and its principal scientist for physical chemicals have left the organisation this year. A fifth position is believed to have been downgraded from a scientific to an advisorial role.

"This is absolutely the worst thing [to happen] to water management in decades," said Stuart Khan an Associate Professor at UNSW and a water contamination expert. "There's essentially only junior scientists left.