"Recent fee increases may constitute indications of an unlawful restriction of competition," the agency said.
Microsoft 365 is widely used "by private businesses as well as numerous government agencies, public companies and other government-related bodies", it added.
The US software giant has faced numerous regulatory battles in Europe over the years concerning claims of market dominance, which it contests.
"Microsoft is committed to complying with Swiss competition law and will cooperate with the Swiss Competition Commission in its preliminary investigation," a spokesman told AFP on Thursday.
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