The company has abused its market position over the past five years, according to CNMC in a press release.
Booking's actions through "unfair business terms" have negatively affected hotels in Spain and limited competition from other online travel agencies.
The booking giant, which is headquartered in the Netherlands, dominates the online market for hotel bookings and is a subsidiary of the American Booking Holdings Group. In Spain, the market share is estimated to be between 70 and 90 percent.
Hotels that want to be visible on booking.com must accept Booking's terms.
The terms include, among other things, that hotels are prohibited from offering rooms on their own websites at a lower price than on Booking, while Booking can unilaterally lower prices.
Another flaw that leads to an uneven competitive situation, according to CNMC, is that the hotels' exposure is affected by their total number of bookings and profitability for Booking. This means that hotels are encouraged to opt out of other booking systems, according to CNMC.
The fact that Booking is subject to Dutch law is another aspect that complicates potential disputes in Spain.
Booking has two months to appeal the authority's decision.