During the investigation, "60 Minutes" found that several of the principals of a number of the schools allegedly built and funded by CAI where empty or built by others, while several school principals said they had not received money from CAI in years.
The CBS report also alleges that the CAI spends more donor money discussing the buildings of schools in Afghanistan and Pakistan in the U.S. than it does on actually building them -- while one charity group alleges 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 CBS.
In a statement released by Mortenson via the CAI on Friday, the author and humanitarian defended himself, his organization and the integrity of his work.
"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 has built schools as a cause of the controversy, stating that "Afghanistan and Pakistan are complex places, torn by conflicting loyalties, and some who do not want our mission of educating girls to succeed."
"Three Cups of Tea" was co-authored with David Oliver Relinhis and has sold more than 3 million copies worldwide since its 2006 release by Penguin Books.