In an interview with the Neue Zürcher Zeitung newspaper, the rightwing politician said that Switzerland should instead focus on improving its bilateral agreements with the EU, of which there are over 100.
Maurer's comments come just days after foreign minister Ignazio Cassis, speaking on the sidelines of the World Economic Forum meeting in Davos, repeated the government's intention to conclude an agreement as soon as possible.
The planned framework agreement would resolve certain institutional questions regarding Switzerland's bilateral arrangements with the EU, for example the role of EU courts in dispute resolution.
Maurer warned against rushing to conclude the agreement before the EU has finalized Brexit negotiations with Britain, saying it was not the Swiss way to proceed so quickly.
Last November then Swiss President Doris Leuthard held a meeting in Bern with EU Commission President Jean-Claude Juncker aimed at making progress on the institutional framework accord, which they had hoped to complete by the end of 2017.
But just before Christmas, a row broke out between the two sides that will have to be dealt with before they can move forward with negotiations.
Leuthard slammed an EU decision to limit Swiss financial access to its markets as “discriminatory”.
Next Wednesday the federal government is expected to set out its negotiation strategy with the EU, the Swiss news agency SDA reported.