One of the hardest-fought marketing battles in the airline industry doesn't involve discount fares or frequent flier programs. It's a battle over computer reservation systems.

In just a few years, these systems have become critically important tools for airlines. They have radically transformed the distribution system through which airline tickets are sold, and offer carriers undreamed-of opportunities for fine-tuning their marketing.

In 1978, the year the skies were deregulated, the airlines carried about 235 million passengers, and travelers typically booked their own flights. Travel agents handled about 38 percent of the volume.

This year the airlines are expected to carry more than 415 million passengers. Travel agents using computer reservation systems will sell most of those tickets -- more than 80 percent for domestic trips and more than 90 percent for international flights.

The major airlines are becoming technology companies in addition to transportation companies. The computer operation "is the heart of the airline. The whole airline couldn't operate without it," according to Barry A. Kotar, president of the Allegis Corp. subsidiary that runs United Airline's Apollo computer reservation system.

As the importance of these systems has grown, so have concerns about their use. Other airlines, which pay transaction fees for tickets booked through one of the systems, have complained that those fees are too high, that the contracts binding them to CRS vendors are too restrictive and that the systems may give the airlines operating them an unfair advantage.

This year the Department of Transportation announced it would investigate airline-owned systems with an eye toward determining whether airlines were abusing the power the systems confer -- a charge often levied by airlines that don't have systems. Members of Congress also have expressed concerns, and 13 carriers have filed suit against American Airlines and United, charging the two with using their systems in an anticompetitive way.

"It's probably one of the most important areas in aviation economics right now in terms of competitive relationships between carriers and the effect on consumers and travel agents," said Matthew V. Scocozza, DOT's assistant secretary for policy and international affairs. And that is not all. "My whole career has been in transportation, and this has probably been one of the most complex transportation problems I have ever worked on."

Five airlines have computer reservation systems, and two -- American and United -- overwhelmingly dominate the market. According to report by the Department of Justice to Congress in 1985, American's Sabre system and United's Apollo system, had 46 percent and 28 percent of agency revenue -- a combined market share of 74 percent. American and United began marketing their systems during the 1970s, a few steps ahead of most other airlines in recognizing their potential.

Three other systems have smaller shares of the market. According to the Justice Department study, Eastern Airline's System One and Trans World Airlines' Pars system each had 10 percent of agency revenue in 1985, and Delta Airline's Data II system had 6 percent.

When Texas Air bought Eastern last year, the crown jewel in the transaction was System One. Building a computer reservation system from scratch is expensive and difficult. Texas Air got its hands on an existing system, as did Northwest Airlines, which paid $140 million for a half interest in Pars last year. Allegis, which is selling off a number of nonairline subsidiaries in an effort to prevent a takeover, said last month that it will also sell an interest in Apollo.

The nation's largest airline company and the parent corporation for Continental and Eastern airlines, Texas Air dominates the airline industry in many respects. Its low labor costs have forced other airlines to rewrite their own labor agreements, and its deep discount fares have set the pace for pricing. But in this arena, Texas Air is the scrapper, trying to increase its share in a saturated market.

"Like any other business, when there are profits to be made, it's going to bring other competitors in," said Kotar. "The money is there, but you have to have critical mass. You have to invest a lot of money" to profit from the systems. United has spent $300 million developing its system.

"There's not any unplowed ground out there for the new farmer, so the new farmer is going to have to take away somebody else's ground," said Joe Stroop, a spokesman for American.

Texas Air has been plowing that ground agressively, offering incentives to convert and helping travel agents who want to switch systems either by buying out the agency's contract with a competitor's system or by helping agencies to litigate.

System One is involved in 10 cases in which travel agents and either American or United are litigating over how much the agencies owe the airlines for canceling their systems before contract expiration dates. "With the dominance the two carriers {American and United} have, you have to pursue it this way," said Richard E. Murray, president and chief executive officer of System One Corp. "We're determined to continue this confrontation, if you want to call it that."

Texas Air's airline subsidiaries, Continental and Eastern, have about 20 percent of airline traffic measured by revenue passenger miles. System One believes it should have a similar share of the CRS business, he said. "There's a lot at stake here, and we know the travel agents are ready for a change. We're going to continue our effort until we get at least to our market share."

As competition heats up the products are likely to improve. Both as a result of competitive pressures and improved technology, the airline companies are bringing out improved versions, Kotar said.