Following routine testing it was found that there is a possibility of legionella at Woodhill House in Aberdeen.
The bacteria can cause pneumonia-type symptoms leading to illnesses including Legionnaires disease.
However, no member of staff has fallen ill.
The majority of staff at the council have been working remotely due to the pandemic. A small number have been back in the building.
An Aberdeenshire Council spokesperson said: “Specialists are on site cleaning, flushing and re-testing the water. As a result, the building will be closed until the all-clear is provided.
“Plans were put in place to move staff who must have a presence in an office, and Public Health advice is being shared with colleagues.
“Limited staff and partners are present in the building currently, and have been advised by their line manager of what to look out for.”