The most severely affected area is the stretch of the Rhine River that runs from Lake Constance to the Rhine Falls, where barrels of dead grayling have pulled from the river since the weekend.
"We have been watching dead fish for several days floating down the Rhine. We had to recover about 1,000 kg from the river," Andreas Vogeli, an official with the hunting and fisheries department in northern Schaffhausen canton, told RTS.
The cold-loving grayling, a member of the salmon family, can struggle when water temperatures exceed 20 degrees Celsius (68 degrees Fahrenheit), but certain areas of the Rhine have recorded temperatures above 27 degrees Celsius in recent days.
During a 2003 heatwave, 90 percent of Switzerland's grayling population was wiped out, Presstv reported.
Samuel Grundler of the Swiss fisheries association said that the situation was "very precarious in many small and medium size stretches of water."
"We have done everything in our power," he told RTS.
The emergency measures include transferring fish to cold-water basins when possible.
"We rescued fish from hundreds of kilometers of streams and transferred them to other waters," fishing and hunting supervisor in Zurich canton, Urs Philipp, told the public broadcaster.
While southern Switzerland has seen unusually high temperatures in summer, water conditions there have not yet resulted in widespread fish mortalities, officials said.