"We should implement our own rules in regards to immigration from the EU, if we cannot come to a common agreement with the EU," Alfred Heer said.
He stressed that despite the decision to put a cap on EU migration, EU citizens are still welcome to the country, but they should not end up in the Swiss social system as over proportionally as the case is today.
"I think the EU will not be happy if we restrict the free access however they cannot do too much about it," he said.
Heer also reminded that one of the reasons for the United Kingdom's vote in favor of leaving the European Union was the mass migration of the Europeans to the country.
The long-lasting negotiations between Brussels and Bern were put on hold earlier this year because of the United Kingdom's referendum on its EU membership, with EU officials asking Switzerland to wait until the Brexit issue had been clarified.
At a referendum held in February 2014, Swiss voters backed introducing quotas on EU migration. The vote jeopardized aspects of the 1999 EU-Switzerland treaty, which gives Switzerland favorable access to EU markets in exchange for eased entry of the EU workforce to the country.