The leader was speaking during a meeting with Swiss President Johann Schneider-Ammann in Berlin on Wednesday, their fourth meeting this year.
“If I was a Swiss citizen, I wouldn't be happy about being judged in an entirely different light due to a decision taken in a totally different country,” news agencies reported Merkel as saying.
Germany's position towards Switzerland has not changed following the Brexit referendum, the chancellor added, saying that the two situations “are completely different things”.
“Negotiations with Switzerland should be conducted as though there was no Brexit,” she said.
Merkel added that it was in Germany's interest for Switzerland and the EU to come to a satisfactory agreement due to the number of Germans who work across the border in Switzerland.
Her stance will be welcomed by the Swiss government, whose attempts to find a way to implement immigration limits -- approved by the public in a 2014 vote -- without contravening the EU principle of free movement have arguably been complicated by Britain's decision to leave the EU.
The EU's negotiations with Switzerland have been overshadowed by Brexit since Britain's June referendum, with many commentators feeling the EU is loathe to give any concessions to Switzerland that it would then be forced to grant to Britain.
In September EU Commissioner Jean-Claude Juncker admitted that Brexit had complicated the situation and that there would be no common immigration/free movement deal for the two countries.
Switzerland has until February 2017 to find an mutually agreeable solution with the EU, or it may be forced to act unilaterally, risking its raft of bilateral agreements with the bloc.
Following Wednesday's meeting with Merkel, Schneider-Ammann said he was “optimistic” that a solution would be found by the end of the year.
However Merkel remained tight-lipped over whether she would support Switzerland's current plan to favour a “light” solution that would impose temporary immigration limits in certain job sectors or regions only, said Le Temps.