Mortenson shot to international fame with the book, which describes his getting lost in an effort to climb K2, the world's second-highest peak, being rescued by Pakistani villagers in the village of Korphe and vowing to return there to build a school for local girls.
He also claims to have been captured by the Taliban and held for several days before being released.
Another best selling-author, however -- Jon Krakauer of "Into Thin Air" fame -- told a CBS "60 Minutes" investigation that aired Sunday that the story is not true.
"It's a beautiful story, and it's a lie," Krakauer tells the program.
"Three Cups of Tea," co-authored by writer David Oliver Relin, stayed on The New York Times best-seller list for four years after it was first published in 2006, becoming a global publishing sensation that has sold more than three million copies and been translated into 47 languages.
CNN.com interviews Greg Mortenson in 2008
Mortenson is also the author of the 2009 sequel "Stones into Schools: Promoting Peace with Books, not Bombs, in Afghanistan and Pakistan," which was another Times best-seller.
Both books recount Mortenson's quest to bring schools to some of the remotest parts of Pakistan and Afghanistan on the theory that education -- especially for girls -- is the best way to end the scourge of the Taliban and other extremists in the region. Mortenson's publisher, Penguin Books, modestly describes him as "a real-life Indiana Jones."
Mortenson's quest to end extremism through education has made him a darling of the U.S. military. A photograph in "Stones into Schools" shows U.S. President Barack Obama's top military adviser, Chairman of the Joint Chiefs Adm. Mike Mullen, opening a girls' school in northern Afghanistan with Mortenson in 2009.
Krakauer is a climber and former donor to Mortenson's charity. CBS said he was one of Mortenson's earliest backers, donating $75,000 to his cause, but withdrew his support over concerns the charity was being mismanaged.