Simonetta Sommaruga said a "foreign authority" provided the information, but did not disclose which one.
She said there was no indication that an attack was planned.
Geneva police have said the raised alert is linked to the Europe-wide investigation into the Paris attacks.
However, Switzerland's federal police said they were not connecting the current operation in Geneva to the attacks.
A report by the Tribune de Geneve newspaper on Friday said (in French) that police had arrested two men of Syrian origin and that traces of explosives were found in their car, but there was no official confirmation of the report.
"The Swiss government received information from a foreign authority regarding a potential IS cell in the Geneva area," Ms Sommaruga told a news conference.
"Federal authorities examined this information and shared it with the local police. There is currently no indication that there was a concrete attack planned."
Reports in Swiss media said the intelligence had originally come from the United States.
Daily newspaper Le Temps, quoting a source close to the investigation, said US intelligence had identified three jihadist cells in Chicago, Toronto and Geneva.
Pictures of four individuals had been circulated to police, the source said, adding: "We do not know their names, we do not know where they came from. They apparently are using noms de guerre."
On Thursday, security was stepped up outside synagogues, the UN building and the French ambassador's home, as well as train stations, the airport and similar places.
The number of police on the city's streets has been increased.
UN spokesman Michele Zaccheo said there was "no specific threat to the UN in Geneva or its personnel".
The border with France runs through the outskirts of Geneva.
IS said it carried out the attacks in Paris on 13 November which killed 130 people.
Two men linked to the attacks - Salah Abdeslam and Mohammed Abrini - are still on the run and investigations have been launched in several European countries.
A raised security alert in the Swiss city of Geneva was triggered by a warning that a cell of so-called Islamic State (IS) was in the area, the country's president says.