The bacteria that cause Legionnaires' disease have been found at several sites in the new Hong Kong government complex after one minister fell ill, in a major embarrassment for the authorities.

The health department Tuesday said nine water samples taken from various places in the buildings, including the chief executive's office, tested positive for Legionella, which causes Legionnaires' disease, a severe form of pneumonia.

The checks at the HK$5.5 billion ($708 million) brand new harbourfront complex, which opened in August last year, were prompted after Education Minister Michael Suen came down with the potentially fatal illness.

Suen was in hospital for nearly two weeks and was discharged last week, but the level of Legionella bacteria found in a tap inside his office washroom was about 14 times more than what is considered safe.

Health authorities said checks also found the bacteria in other parts of the building, including the washrooms of several other ministers, the canteen and a bakery, and ordered a massive disinfection operation.

"This is more than embarrassing. It's really a shame," said Cyd Ho, a pro-democracy legislator.

Ho blamed the government and Chief Executive Donald Tsang, whose term expires in June, for rushing to open the new building which she said had compromised the cleaning and sanitisation work.

"Everyone was under pressure to accommodate the wish of one person just because of his will to move in as soon as possible so he could deliver his last policy address (in October) in the new complex," she claimed.

"This disease normally occurred only in very old buildings so when it's found in a new building, it's a shock to everybody," Ho told AFP, urging Tsang to apologise to the more than 3,000 government staff who work at the new compound.

Microbiology professor Ho Pak-leung told the South China Morning Post that the presence of the bacteria was worrying and it could lead to severe pneumonia, with a fatality rate of 30 percent.

Legionella bacteria thrive in warm water, and can be found in water tanks, cooling towers, whirlpools and spas. They may be spread through exposure to contaminated water droplets, but cannot be passed from person to person.

Despite the findings, the government has downplayed fears and said staff can work as normal.

"Finding Legionella bacteria in the water is not equal to an outbreak of the Legionella disease," the government's centre for health protection controller Thomas Tsang said, according to The Standard newspaper.

Authorities said disinfection work and installation of water filters would contain the bacteria, and that water samples would be tested again after the work.

Water filters and alcohol gel dispensers have also been installed in washrooms while buckets of clean water were brought into the government offices on Tuesday afternoon, according to public broadcaster RTHK.

Legionnaires' disease was named after an outbreak occurring in a Legion Convention in the United States in 1976.