Airline United Continental will permanently retire flight numbers 93 and 175, the designations of the United flights hijacked in the terrorist attacks of September 11, 2001, after they reappeared on a computer reservation system.
The numbers were loaded erroneously May 16 because of an oversight and were removed today, Chicago-based United Continental said.
Neither number will be used again, said the airline, which was rebuked by unions representing pilots and flight attendants over the reuse of the numbers.
"The flight numbers were inadvertently reinstated in our system," an airline spokesman, Rahsaan Johnson, said in an email.
"We have already taken steps to remove them and apologise for the error."
Numbers 93 and 175 were assigned to Continental-operated flights that were also going to carry United's booking code, said Airlineroute.net, which tracks schedule data.
United and Continental merged in October and will operate separately until regulators grant them a single certificate.
United Flight 93 crashed in a Pennsylvania field as passengers tried to retake the cockpit from hijackers who seized the Boeing 757 en route to San Francisco from Newark, New Jersey.
Flight 175, a Boeing 767, was crashed into the World Trade Center's south tower on a flight to Los Angeles from Boston.
Terrorists also crashed American Airlines Flight 11 into the north tower of the World Trade Centre and Flight 77 into the Pentagon during the attacks. American's parent AMR does not use those flight numbers.
The attacks killed 25 flight attendants and 10 other airline employees on the four planes, the Association of Flight Attendants said.
"We will never forget the heroic actions of our friends and colleagues or the pain of their loss," Greg Davidowitch, president of the AFA unit at United, said in a statement.
United's chapter of the Air Line Pilots Association said the planned reuse of the flight numbers showed "insensitivity and unconscionable disrespect".
"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," Captain Wendy Morse, the ALPA chapter chairman, said.
Almost 3000 people died in the attacks orchestrated by bin Laden, who was killed this month by US special forces who raided his hide-out in Abbottabad, Pakistan.