Denver-based Frontier Airlines has been doing everything it can of late to convince its customers to book directly on its website, FlyFrontier.com, and now its relationship with Expedia Inc. appears to have become a temporary casualty of that initiative.

The Expedia-Frontier contract expired over the weekend, and Frontier announced today that its flights are not available on Expedia and Hotwire sites, although they are still being offered to Expedia’s corporate clients through its corporate travel agency, Egencia.

“This was an economics-driven decision,” says Frontier spokesperson Kate O’Malley. “When customers book directly at FlyFrontier.com, it helps to keep our costs low, thus allowing us to continue to offer affordable fares to our customers.”

“Unfortunately, we were unable to reach agreement with Expedia to continue offering our schedules and fares on their website,” O’Malley adds.

Expedia spokesperson Mallory Seubert says Expedia “elected to pull Frontier flights and fares from select Expedia-brand and Hotwire sites,” when the two sides couldn’t come to an agreement, and that a new contract is under negotiation.

“We are currently working to achieve a mutually beneficial agreement between Frontier and Expedia, Inc. that will allow us to deliver the most competitive, cost-efficient option to travelers,” Seubert says.

“We value our relationship with Frontier, and we look forward to offering their full content on our Expedia and Hotwire sites,” Seubert adds. “All Frontier flights are currently available on Egencia.”

Neither Frontier nor Expedia would discuss the details of what led to the impasse.

Frontier has been trying to get more leisure travelers to book directly on FlyFrontier.com, where its costs are the lowest. Since September, passengers booking flights on FlyFrontier.com pay fewer fees, can get assigned seats earlier, and earn more frequent flyer miles than travelers booking Frontier flights elsewhere.

Expedia and its airline and hotel partners have skirmished over contract renewals from time to time. However, it is likely that the two sides will eventually come to an agreement as Frontier benefits from Expedia’s reach.

American Airlines tickets were absent from Expedia sites for three months in 2010, reappearing in April when the two sides came to an agreement.

The conflict with Frontier will have much less of an impact than the one with American as Frontier, a subsidiary of Republic Airways, is a much smaller airline.

Frontier’s direct-booking initiative likely won’t be as extreme as that of Southwest Airlines.

Southwest.com is generally the only website where leisure travelers can book the airline’s tickets online. While absent from Expedia and Hotwire, Frontier tickets are currently available on online travel agency sites such as Priceline, CheapOair, Orbitz, and Travelocity.