Exports in the first three months of the year fell by 1.4 percent to 50.6 billion francs from the first quarter of 2014, the federal customs administration (FCA) said in a report.
Imports, on the other hand, dropped by 4.4 percent to 42.4 billion francs, the FCA said.
After the Swiss National Bank in January abandoned a policy of maintaining a euro floor of 1.20 francs currency traders have bid up the franc.
On Thursday morning the euro was trading at 1.037 francs, having strengthened slightly as fears over a Greek exit from the eurozone eased.
The effect of the stronger franc cut the cost of imports by 5.1 percent in the first quarter when in “real terms” imports edged up by 0.8 percent, the report said.
The FCA said virtually two-thirds of the Swiss export sector saw a drop in export sales and prices for their products.
The paper and graphic arts sector was the worst hit with a 13.1 percent reduction, followed by plastics (down 8.8 percent) and machinery and electronics (6.5 percent).
Among other findings of the report, exports to the US rose for the 14th consecutive quarter.
The American market has been less impacted than the eurozone because of the relative strength of the US dollar.
Also exports from the watchmaking industry rose 3.1 percent in the first quarter from the same period a year earlier, while the jewellery sector recorded the biggest increase at 21.7 percent.