Wednesday’s “test came back positive and the president went into self-isolation this morning as soon as he learned of the test result,” a government statement said.
“Mr Cassis has no symptoms and is in good health.”
The former cantonal doctor, aged 60, who holds the annually-rotating Swiss presidency alongside his foreign affairs brief, will return to his office next week.
Cassis struck an upbeat tone on Wednesday as he announced Switzerland was joining European countries including Austria, Britain, the Netherlands, Denmark and Norway in dropping almost all of Covid-19 restrictions.
“The light is definitely there on the horizon,” he told a press conference, adding it was time to “learn to live with the virus”.
“We shouldn’t be afraid of a return to normal, but we shouldn’t be too enthusiastic either,” he said.
The only remaining coronavirus requirements in Switzerland are the obligation to self-isolate for five days after a positive test and to wear masks on public transport and in healthcare institutions.
To enter the country, it is no longer necessary to provide proof of vaccination, recovery or a negative test, or complete an entry form.
Switzerland, population 8.6 million, has registered more than 2.6 million Covid-19 cases and over 12,500 deaths during the pandemic.
At around 20,000 a day, recorded new infections are now around half of the peak witnessed towards the end of January.
However, the case rate is still higher than in the surrounding European Union. Nearly 69 percent of Swiss residents are fully vaccinated and 41 percent have had a booster dose.