President Doris Leuthard said a referendum was needed to sort out how the nation worked with the European Union.
Ms Leuthard said: “The bilateral path is important. We must therefore clarify our relationship with Europe. We have to know in which direction to go.
“Therefore a fundamental referendum would be helpful.”
Switzerland has a unique relationship with the EU.
While it is not a member of the EU it is part of the Schengen zone and has numerous bilateral agreements with the bloc.
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Brussels and Bern are working to cement the relationship with an overall deal but talks hit problems this week with the EU only offering limited access to stock exchanges which angered Swiss officials who threatened to retaliate.
Ms Leuthard told the Swiss newspaper SonntagsBlick: “We can strengthen the co-operation with India and China, but the EU remains central.
“We need a mechanism and regulated relationship with the EU. That would also prevent political games like we are witnessing at the moment.”
She added the EU’s stance over limited stock exchange access was not acceptable.
She said: “Of course, the differences with Brussels are now in focus. Here our attitude is clear: For the EU to link such a technical dossier like stock exchange equivalency with a political question like the framework agreement, that won’t do.”
Before Christmas the EU offered the Swiss stock exchange access to the EU market for only one year despite recently granting the US, Hong Kong and Australia access for an unlimited time.
At the time Ms Leuthard said: “The EU is acting this way to weaken the Swiss financial centre.
“It is unfounded and unacceptable to link this technical issue to the institutional question.”
The commission argued that in comparison with these three countries, “the scope of the Swiss decision is much greater, as the trading of Swiss shares in the EU – and vice versa – is more widespread.”
A commission official said in Brussels: “This decision should not come as a surprise.”
If the Swiss did hold a referendum this could be problematic for the EU as the Swiss parliament’s biggest group is the Eurosceptic Swiss People’s Party with 65 members.