After it was removed from the site during cleanup, the flag flew on U.S. ships serving in the war in Afghanistan. Then, in March, it was returned to New York City officials.
But the flag that city officials preserved measures 5 feet by 8 feet. The flag the firefighters raised on Sept. 11 measured 4 feet by 6 feet, according to its original owners.
"It's just a really awkward and difficult situation," said Lark-Marie Anton, a spokeswoman for New York Mayor Michael Bloomberg. "What it represents is really what's important."
Bloomberg has asked city fire officials to investigate what happened to the flag. Officials say they are unaware of anyone claiming to possess the original.
The flag came from a yacht, the Star of America, which was in a Hudson River marina near the World Trade Center that day. Firefighter Dan McWilliams took it from the yacht and walked back to Ground Zero, where he and two colleagues, George Johnson and Bill Eisengrein, raised it on a slanted pole.
The scene was captured by Thomas Franklin, a photographer with The Record of Bergen County (N.J.), and distributed worldwide by The Associated Press.
The discrepancy about the flag size was discovered last month when the yacht owners, Shirley Dreifus and her husband, Spiros Kopelakis, borrowed the flag for an event on board the Star of America.
The couple had been preparing to formally donate the flag to the city when they said they noticed the flag was too big to be theirs.
"It's a mystery," Glen Oxton, an attorney representing the owners said Thursday in The Record. "Who knows what happened to it after the firefighters put it up and the photograph was taken? There was so much activity down there."