When you buy an airline ticket through a discount online travel Web site, are you getting the best deal out there?

Not necessarily, some top airlines say, arguing that the country's most popular independent travel sites give preferential treatment to the carriers that advertise with them, displaying them on the sites' listings first.

The independent online travel sites deny these accusations of favoritism, as the entities raise the same concerns about new airline-backed Web sites that are starting up over the next year.

Consumers May Lose in the End

But as the airlines and the independent sites that help book flights battle over the placement of air fares, the consumer may end up the loser. Consumer advocates argue that travelers may pay a higher fare, or take a less convenient route, because they don't know that other options are available.

In one example of the rising tensions between the airlines and the travel Web sites that display their fares,

Northwest Airlines

(NWAC)

pulled all of its flight information off

Lowestfare.com

earlier this month after talks broke down a couple weeks ago between the carrier and the discount travel site, which is owned by financier Carl Icahn.

Asserting that the Web site's flight listings favored competing carriers, Northwest, the world's fourth-largest airline, cut off Lowestfare's access to its flight information for a week and has threatened to restrict the fares offered to other independent travel sites as well. That's a move that could become more common with the introduction of airline-owned Web sites like the newly introduced

Hotwire

, as well as

Orbitz

, which is

set to begin operations next summer.

Northwest's action also raises an issue that federal transportation officials must grapple with as they consider whether, and how, to regulate online travel sites: Should airlines be forced to offer all their inventory to every online site? If airlines restrict their best fares to the sites they own, it could threaten the future of independent travel sites.

Independent sites insist that they show the best fares and flight routes available to them. But there are some fares -- like e-fares, which are offered exclusively through the airlines' own sites (and, potentially, through the new airline-backed sites) -- that they cannot access.

The sites contend that their displays vary now because they depend on different computer reservations systems and use their own formulas for sifting through thousands of flight combinations in search of the lowest fare. Airlines may also offer exclusive discounts to specific sites through advertising arrangements.

Study Finds Disturbing Results

But Northwest's contentions were backed by a study that found "disturbing evidence" of favoritism toward particular airlines on the country's four most popular sites:

Travelocity

(TVLY)

,

Expedia

(EXPE) - Get Report

, Lowestfare and

CheapTickets

.

The study found that

TransWorld Airlines

TheStreet Recommends

was listed as the first choice 50% of the time on Lowestfare's site, when the other top three sites listed TWA first no more than 23% of the time. That may be due in part to a legal settlement between Icahn, a former TWA chairman, and the airline, which gives his site access to a number of discounted TWA fares.

Northwest Airlines, an investor in Hotwire and Orbitz, lifted its flight information restrictions after Lowestfare agreed to offer more display results and reduce duplication in the airlines listed. But David Lovely, director of marketing and communications at Lowestfare, denies that the site gave preferential treatment to any carriers.

Al Lenza, Northwest's vice president of distribution planning, said restricting inventory is a measure the airline felt forced to take. "It was not an ordinary course of business," he said.

"What we don't want is for the site to hold itself out as giving customers the best fare, but on the back end it's displaying the best fares from carriers who give it the most (money)," Lenza said.

Other carriers also express similar frustrations with the way in which flights are displayed on various sites.

"There's a tremendous amount of bias steering you toward a particular airlines on these sites," said one

Continental Airlines

(CAL) - Get Report

executive.

After an extensive months-long study of the four sites, Bill McGee, editor of

Consumer Reports Travel Letter,

said that while the testing did not yield conclusive results, "they did reveal some telling evidence that travel sites may not be totally objective at all times."

On Travelocity,

Consumer Reports

researchers said the site's featured airline, which receives full-color advertisements linked to specific cities or airports, was listed first 48% of the time and dominated other listings.

Terry Jones, chief executive of Travelocity, denies there is any bias on his Web site, as defined by the

Department of Transportation

. "We rigorously conform to those rules and have since they were put into place."

Since the

Consumer Reports

article was published, Travelocity has gone so far as to ask

Ernst & Young

to audit its Web site to ensure its methodology is not biased. "It's unfortunate they (

Consumer Reports

) implied we did something wrong when we did not," Jones said.

The discrepancies among fare listings on major independent travel sites were wide enough to prompt the publication to recommend that consumers shop around for the best fare, rather than rely on one-site shopping. Until there are regulations in place, that may be the best option for consumers.

The concern about favoritism in providing fares to consumers actually dates back to the 1980s, when the

Department of Transportation

devised rules for computer reservations systems, which store flight data, after receiving complaints about biased displays from travel agencies and airlines. The regulations were aimed specifically at reservation systems then owned by airlines, so that such systems couldn't unfairly promote their airline owners.

Transportation department officials are now looking at expanding those regulations to include all online travel sites. But a top official involved in the process said that while the department is committed to getting a lot of the rule-making done by the end of the year, it is not likely to have new rules in place before next summer.