Foreign Minister Micheline Calmy-Rey says Switzerland should consider a special type of European Union membership as one of several strategic options.
But Interior Minister Pascal Couchepin said the current policy of strengthening ties through bilateral treaties with Brussels would go a long way.
Calmy-Rey said a status quo in relations with the EU was unrealistic.
"We have to prepare for all eventualities. New questions will arise, also within the EU," Calmy-Rey told the SonntagsZeitung newspaper.
She said one of the options was to include the 16 bilateral treaties with Brussels in a framework agreement or to seek "membership light".
Switzerland could for instance apply for membership but insist on opting out of the common European currency, she said.
Calmy-Rey said a framework accord could pave the way for a joint institutional body to discuss practical points about the bilateral accords or even tackle certain foreign policy issues together.
Her statements appear to contradict comments made by Couchepin on Saturday. He said Switzerland's current policy of bilateral treaties would remain a priority for some time to come.
But both ministers in the four-party government agree that Switzerland wants to keep a high degree of autonomy in its foreign policy.
"We will continue to pursue our own interests, but [Switzerland and the EU] have common goals in the Balkans region or the Middle East," said Calmy-Rey.
Last Wednesday the Swiss cabinet decided not to withdraw the Swiss application for EU membership lodged in 1992, despite calls by the rightwing Swiss People's Party.
The request was frozen in the wake of voters' rejection of the European Economic Area treaty in the same year.
The Swiss government is due to consider several foreign policy options next year based on the findings of an official report.
Switzerland negotiated 16 bilateral accords with the EU covering issues including trade, labour, transport, taxation and security.
This year the Swiss electorate approved a plan for closer cooperation on asylum and police matters (Schengen/Dublin accords) as well as extending a labour accord to the ten new EU member states.
swissinfo with agencies
In 1992 Switzerland applied for negotiations on EU membership, but the request was frozen in the wake of voters' rejection of the European Economic Area treaty.
Switzerland and the EU concluded 16 bilateral accords.
Earlier this month the government decided to not to withdraw the request, but made full EU membership a long-term policy option, rather than a strategic aim.
The cabinet also agreed to the opening of an EU embassy in Switzerland.