Confusion bordering on chaos overtook the nation's air travel system this week as major carriers slashed fares on some heavily traveled routes while raising fares on others.

One-way fares from New York and other northern cities to Florida and California dropped to $99 on several airlines, but increases of up to 5 percent went into effect on a majority of routes where lack of competition has insulated the carriers from fare wars.

As travel agents and airline ticket offices struggled to keep track of the changes, officials of several lines said their fares were changing almost daily as they adjust them on a market-by-market basis. A spokesman for United Air Lines said an average of 5,000 fare "corrections" per day were being written into United's reservations computers. And of course, varying restrictions accompany most of the discount fares, adding to the complexity of the fare wars.

Many of the fare changes could not be justified on economic grounds, airline officials said, but were needed to boost traffic and revenues in a slack period.

TWA, for example, is charging $99 to fly nonstop from New York to Cleveland and $99 to fly from New York to Los Angeles. "Of course it makes no economic sense whatever," an official of the airline said, "and it's only going to erode our earnings position further. But because there is less and less traffic as the state of the economy limits air travel, we have to hold on to what share we have."

TWA, Pan American, United, Delta, Piedmont and American were among the airlines that increased most fares on most routes by 5 percent. Spokesmen for these carriers said they were generally matching deep-discount fares offered by competitors on routes where they compete directly, but raised fares where the market would bear it.

Eastern Airlines said its increases generally were less than 5 percent. Northwest Orient said it has "not yet" imposed any across-the-board increase.

As examples of the impact of these changes on Washington, the one-way coach fare to St. Louis on TWA rose from $202 to $213. The weekday "supersaver" round-trip fare to Charlotte on Piedmont went from $131 to $138. The one-way coach fare to Boston on Eastern rose from $145 to $150.

Passengers who bought their tickets before the increases were imposed will not have to pay the new fares, airline officials said. Because most travelers do buy their tickets in advance, it could be several months before the airlines obtain the full revenue increases they expect from the new higher fares.

At the same time as most fares have been going up, however, the major carriers have been going after each other in a price war designed to fill seats. Pan American, for example, is offering a $99 fare from Washington to several cities in Florida, New Orleans, Houston, Oklahoma City and the West Coast. These fares will be in effect through Dec. 15 and from Jan. 10 to Feb. 6 -- but in between, during the peak holiday season, Pan Am will charge the new higher fares. Eastern said it would match Pan Am's fares, and Delta said it would do so on routes where it is directly competitive.