The improvement notice does not mean the National Museum of Scotland has been identified as the source of the outbreak of Legionnaires' disease.
The museum can appeal against the notice within the next 21 days.
Tests have confirmed that there are no issues with Legionella in our cooling towers.
Following a routine inspection by the Health and Safety Executive and the City of Edinburgh Council Environmental Health, both organisations confirmed they are satisfied with our documentation and procedures.
Two other organisations, pharmaceuticals firm Macfarlan Smith and the North British Distillery, have already been served with improvement notices.
These do not mean any of the cooling towers are the source of the outbreak.
The Scottish Health Secretary says there are 24 confirmed and 37 suspected cases of Legionnaires' disease. She expects this figure to rise.
Legionnaires' is a disease that strikes fear in people and its history shows it can be deadly.
The Scottish Health Secretary will today update MSPs on efforts to deal with a deadly outbreak of Legionnaires' disease in Edinburgh.