The CFIA says it’s the first time it has confirmed the disease in Canada.
Whirling disease is caused by a parasite that causes skeletal and neurological damage in young trout and salmon.
The fish move forward in a corkscrew pattern instead of swimming normally and there is a high mortality rate.
Parks Canada says it has closed the area around Johnson Lake and banned any recreational activities to reduce risk of the disease spreading.
The parasite is not harmful to humans or mammals, but can be transmitted to other water bodies by fish and fish parts or by gear used for swimming, paddling, boating and angling.
Parks Canada is working with the province and the CFIA to test watersheds inside and outside the park to see if the disease is present anywhere else.
The Alberta Environment Department says it has taken about 700 samples from water bodies downstream from the park and sent them to a testing facility. This is in addition to ongoing tests by the CFIA. Results are expected in early September.
Parks Canada is reminding visitors that fish and fish parts should be properly disposed of. All equipment and gear such as boats, trailers, waders, boots, float tubes and fins should be cleaned before and after being used.
Whirling disease has been observed in the United States since the 1950s and is prevalent in the western and northeastern states.