It said it was working with the company and environmental health officers to help prevent further transmission of the virus – and identify where the cluster came from.
The news came after reports of a number of cases had been detected in connection with the depot at St Leonards.
The company denied that the workplace was the source.
A spokesperson for Stagecoach East Scotland: "These claims are completely untrue.
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"The safety and well-being of our employees and customers is our first priority, and we have strict protocols in place around the management of COVID-19.
"There have been a small number of cases in the depot in recent weeks, and there is no evidence that any of the cases are linked to workplace transmission.”It said it continued to work with the NHS Fife Health Protection Team and follow all guidance from public health.
The spokesman added: "We have rigorous cleaning regimes in place, as well as making it mandatory for drivers to wear face coverings whilst in the depot.
"There are also numerous sanitising stations, clear signage and one-way systems in place.
"We also have similar measures in place to provide confidence to our customers, such as regular deep cleans as well as touch point cleans throughout the day, face masks being mandatory throughout the journey, ventilation on our services, capacity limits and social distancing."
A spokesman for NHS Fife said: “We are aware of a cluster of COVID-19 cases with possible links to the Stagecoach East Depot in Dunfermline.
"A cluster of seven people have been confirmed as positive for COVID-19 and work is underway to investigate whether some or all of these cases are linked, or whether the virus has been contracted through community transmission.”
He added: “NHS Fife’s Health Protection Team and is working alongside Fife Council’s environmental health service to support the management of the bus depot and help to prevent further transmission of the virus. Based on the information available at present, the risk to the public appears to be low.”