"Exports fell by 4.1 percent to 13.9 billion francs ($15.7 billion)," it said in a press release.
"This evolution is due to the strength of the franc," the customs authorities said.
Amid the public debt turmoil engulfing the European Union, investors have massively bought into the franc, sending it to record highs against the euro and threatening the country's export-led economy, leading the central bank to put a floor on the euro's value against the Swiss franc in early September.
However, the country still managed to have a trade surplus of 808 million francs in August, the customs authorities said, a figure 56.4 percent higher compared to the same month in 2010.
It added that all export sectors had been negatively hit, except for the watchmaking industry.