Spokesman Rahsaan Johnson blamed the reuse of flight numbers 93 and 175 on a "technical error." He said the airline has taken steps to have the numbers removed from its computers.
"We apologize for the error," Johnson said in an interview. "The numbers were inadvertently reinstated."
United flight 93, heading to San Francisco from Newark, N.J., crashed in Shanksville, Pa., killing all 44 people aboard. Flight 175, from Boston to Los Angeles with 65 people aboard, crashed into the south tower of the World Trade Center in New York.
Johnson said the flight numbers went back into use on Monday night. The airline had stopped using the flight numbers shortly after Sept. 11.
A notice posted Tuesday on the airline schedule website Airlineroute.net said United planned to reactive the two flight numbers Saturday, but that Continental Airlines would operate the flights in a code-sharing arrangement. A code share allows one airline to book seats on a flight operated by a second airline. Often the flights operate with the name of the airline that did the booking rather than the airline operating flight.
United and Continental recently merged and became United Continental Holdings Inc., but are in the process of combining operations. Under the merger agreement, the combined airline will fly under the United name.
The notice on Airlineroute.net said the new flight 93 would fly from Houston to San Jose, Calif., and that flight 175 would operate from Boston to Newark.
"Out of respect for those who lost their lives and those who will always remember our heroes, United Airlines must what should have already been done -- immediately and permanently retire these flight numbers," said Greg Davidowitch, president of the Association of Flight Attendants.
The union is competing with the International Association of Machinists and Aerospace Workers to represent flight attendants at the combined United.
Wendy Morse, a United captain and an official with the Air Line Pilots Association unit representing United pilots, said "the thought of anyone among management at United Airlines to even consider reinstating these two sacred flight numbers - on the heels of Osama bin Laden's death - demonstrates a severe disconnect from right and wrong."
AP Airlines Writer Joshua Freed in Minneapolis contributed to this report.