A ministry spokesman said Berset misinterpreted information from the French air traffic control tower prompting an intervention by the French air force last week.
Berset was able to continue his flight with the hired Cessna light aircraft following an identity check and further inquiries, according to the spokesman.
The Neue Zürcher Zeitung newspaper on Tuesday reported that Berset, who has a pilot licence for small aircraft, had taken off from western Switzerland on a private flight over several stages.
He reportedly approached the closed airspace above a command centre of a French military air base about 300km from the Swiss border.
Berset has been in the Swiss news over the past few years over a blackmail affair in a reported extramarital relationship.
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Attempt to blackmail Swiss interior minister under investigation
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A woman who tried to blackmail Swiss Interior Minister Alain Berset last year has been fined after retracting her claims against him, it has emerged.
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