Michael Kotula and his wife booked a hotel room through Expedia eight months in advance of their daughter’s University of Delaware graduation in late May. They reconfirmed directly with the hotel two months before the big event.

Two days before check-in, Expedia told them in an email the hotel was canceling. And when they called the Hilton Wilmington/Christiana in Newark, Del., to complain, Mr. Kotula was told reservations made through travel agencies like Expedia weren’t as secure as booking directly with the hotel.

“I wish I had known before that my reservations with Expedia were built on quicksand,” Mr. Kotula says.

Reservations made by authorized agencies are legally just as secure as bookings made directly with airlines, car-rental firms or hotels, according to hotel executives and industry analysts. But since hotels have to pay commissions for agency bookings, they try to push customers to book directly. And many travelers harbor doubts about the security of using a middleman, and use online travel agencies like Expedia and Orbitz for comparison shopping and then book directly.

Expedia says the hotel was wrong to tell Mr. Kotula there was a difference. “They’re looking for someone to blame,” says Adam Anderson,Expedia’s managing director of industry relations. But Hilton says in a statement that direct booking reservations may be favored when guests are relocated because “it is easier for the hotel to communicate directly to the guest if they had booked directly through Hilton.”

Brad Wenger, general manager of the Hilton Wilmington, referred questions about the handling of the reservation to Hilton. Andrew Flack, Hilton’s vice president of global marketing, referred questions about Mr. Kotula’s reservation to the hotel.

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