During an investigation, watchdog Stefan Meierhans examined commissions paid by hoteliers to the site and found indications of abusive prices, news agency ATS reported on Tuesday.
According to Meierhans, Booking.com was not interested in negotiating an amicable agreement on the issue, therefore he has now opened formal proceedings against the company.
Unless the website decides to enter into discussions, Meierhans will take a unilateral decision to fix commissions at certain rates, a judgement which could be appealed at the federal civil court.
It's not the first time Booking.com has been in trouble with the Swiss authorities.
In October 2015 the Swiss competition commission ruled that the site and others like it were imposing certain contractual obligations on hoteliers that were illegal. They did not allow hoteliers to set lower prices or offer a higher number of rooms through other marketing channels.
Since then Booking.com and Expedia have adopted less restrictive clauses.
Founded in 1996 in Amsterdam, Booking.com is now one of the world's biggest and best-known booking sites, covering hotels and holiday properties in 225 countries around the world.