The Transportation Department yesterday said passengers may not be booked on smaller, commuter airlines by large carriers without being told by the airline doing the booking.

That information must be disclosed by airlines in tickets and in computerized and printed airline schedules rather than obscured by using the same flight designation for both airlines, the current practice.

However, the rule is binding only on airlines, not on travel agents, who book about two-thirds of all domestic flights. If the ticket is purchased from an airline, it must alert the passenger. However, if the travel agent does not tell the passenger that his USAir flight from Washington National to Atlantic City is on a deHavilland Twin Otter operated by Southern Jersey Airways, not a Boeing 737 operated by USAir, there is no way he will know.

The final rule, announced late yesterday, addresses one of the most controversial issues to have arisen among the airlines since deregulation in 1978.

Because of cooperative arrangements between large and small carriers, a ticket shows a passenger that he is changing from one flight to another on the same carrier, when in fact he may be going from a big Delta Airlines jetliner to a small Atlantic Southeast Airways turboprop.

Most major carriers have set up arrangements with commuter airlines, often separately owned and operated, under which the commuters use the flight numbers and airport facilities of the major carriers. The small airline gets the passenger feed and the big airline can easily shuttle passengers to smaller cities that cannot support jet service.

The issue is known as "code-sharing," because of the two-letter code by which airlines are identified in ticketing computers and in the Official Airline Guide, the master schedule book.

United Airlines Chairman Richard Ferris calls code-sharing "the greatest fraud ever perpetrated on the American public." However, United also has code-sharing arrangements because, Ferris has said, it must to compete.

The Transportation Department rejected an outright ban on code-sharing, something that United and some consumer advocates have urged. The rule, which will take effect Dec. 23, requires code-sharing airlines to:

*Identify in ticketing computers and to the Official Airline Guide each flight in which the code is different from the code of the airline actually flying.

*Alert the consumer in any "direct oral communication" that the flight will occur on a different airline than the one indicated.

*Provide frequent notice in advertising to passengers and travel agents of the existence of a code-sharing relationship.

USAir and American, two airlines with extensive code-sharing operations, declined comment until they have read the rule.

Transportation Secretary Elizabeth Hanford Dole said, "This rule will provide balance between the interests of the airlines and the rights of consumers. While code-sharing may have its beneficial aspects for airlines, passengers have the right to know what airline is actually providing the service they will use."

Monte Lazarus, a United Airlines vice president, said, "We would prefer to have nobody able to use the shared designator because it does confuse the public. Notice is a good thing, but notice doesn't always get through to the public in this kind of a situation, and that's the problem."