"It's a beautiful story. And it's a lie," Krakauer told "60 Minutes." "I have spoken to one of [Mortenson's] companions, a close friend who hiked out from K2 with him, and this companion said, 'Greg never heard of Korphe until a year later.'
"If you read the first few chapters of that book, you realize, 'I am being taken for a ride here,'" Krakauer said.
According to the website of the Central Asia Institute, which was co-founded by Mortenson and Jean Hoerni, the nonprofit has established more than 170 schools and helped educate more than 68,000 students, with an emphasis on girls' education.
During its investigation, "60 Minutes" found that several of the schools CAI said it had built and funded were empty or built by others, while several school principals said they had not received money from CAI in years.
The CBS News "60 Minutes" segment also reported that the CAI spends more donor money discussing the building of schools in Afghanistan and Pakistan than it does on actually building them -- while one charity group said that donor money is being used to promote Mortenson and his book.
"In 2002, [Mortenson's] board treasurer quit, resigned, along with the board president and two other board members. ... He said, in so many words, that Greg uses Central Asia Institute as his private ATM machine. That there's no accounting. He has no receipts," Krakauer told "60 Minutes."
Mortenson defended himself, his organization and the integrity of his work, in a statement released Friday through CAI.
"I stand by the information conveyed in my book and by the value of CAI's work in empowering local communities to build and operate schools that have educated more than 60,000 students," Mortenson said.
"I continue to be heartened by the many messages of support I receive from our local partners in cities and villages across Afghanistan and Pakistan, who are determined not to let unjustified attacks stop the important work being done to create a better future for their children."
Mortenson also pointed to sexism in the countries where his organization had built schools as a cause of the controversy.
"Afghanistan and Pakistan are complex places, torn by conflicting loyalties, and some do not want our mission of educating girls to succeed," he said.
"Three Cups of Tea" was co-written with David Oliver Relinhis and has sold more than 3 million copies worldwide since its 2006 release by Viking, a division of Penguin Books.