In 2010, South Asian scholar and anthropologist, Nosheen Ali, criticized Three Cups of Tea in that “it constructs a misleading narrative of terror in which the realities of Northern Pakistan and Muslim life-worlds are distorted through simplistic tropes of ignorance, backwardness and extremism, while histories of US geopolitics and violence are erased.” 
In regard to Mortenson's management style at the Central Asia Institute, Nicholas D. Kristof, normally a supporter of his, has said that Mortenson is "utterly disorganized," and added, "I am deeply troubled that only 41 percent of the money raised in 2009 went to build schools." As a deeper look into Mortenson's business dealings, British journalist Jonathan Foreman wrote in a 2008 Daily Telegraph story that CAI's success is due in part to Mortenson's use of intuition and that he makes decisions at the last minute. Foreman further wrote that Mortenson is habitually late for meetings but that the combination of those traits work well and are important to the success of his work in the Balti region of Pakistan. Baltistanis have no tenses in their language, are vague on their timekeeping, and make their own decisions largely based on intuition.
On the April 17, 2011 broadcast of CBS News' 60 Minutes, correspondent Steve Kroft alleged inaccuracies in Mortenson's books Three Cups of Tea and its sequel, Stones into Schools: Promoting Peace with Books, Not Bombs, in Afghanistan and Pakistan as well as financial improprieties in the operation of the Central Asia Institute. In particular, CBS News disputed Mortenson's claim that he got lost near K2 and ended up in Korphe; that he was captured by the Taliban in 1996; whether the number of schools built and supported by CAI is accurate; and the propriety in the use of CAI funds for Mortenson's book tours. 60 Minutes asked Mortenson for an interview before their broadcast, but he did not respond to their requests.
60 Minutes made the following allegations:
- The events recounted in Three Cups of Tea—Mortenson getting lost on the way down from K2, stumbling into Korphe, and promising to build a school—did not take place.
- The story recounted in Stones into Schools about Mortenson's capture by the Taliban did not occur. His purported kidnappers state he was a guest, and the Taliban did not exist in the country at that time.
- Schools that the Central Asia Institute claims to have built either have not been built, have been built and abandoned, are used for other purposes such as grain storage, or have not been supported by CAI after they were built.
- The amount of money Central Asia Institute spends on advertising Mortenson's books and paying the travel expenses of his speaking tours, including hiring private jets, is excessive relative to other comparable charitable institutions.
Jon Krakauer, a former financial supporter of CAI, has questioned Mortenson's accounts separately and was interviewed for the 60 Minutes segment. The day after the broadcast, Krakauer released his allegations in a lengthy online article, Three Cups of Deceit — How Greg Mortenson, Humanitarian Hero, Lost His Way. In the article, Krakauer documents how he had earlier been captivated by Mortenson's story, had donated substantial sums to CAI, and that he had later heard stories of misconduct and began investigating. Krakauer states that he invited Mortenson to address his allegations, including setting up an interview where Mortenson lives, but Mortenson subsequently canceled the interview.
Mortenson wrote a statement in response to the allegations made against him that was published in the Bozeman Chronicle: "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 further stated, "The time about our final days on K2 and ongoing journey to Korphe village and Skardu is a compressed version of events that took place in the fall of 1993..."
Scott Darsney, a respected mountaineer and friend of Greg Mortenson, wrote an email, subsequently turned into an exclusive article for Outside magazine's online version, as a response to the allegations against Mortenson. Darsney questioned the accuracy and fairness of both the Krakauer piece and the 60 Minutes report. Darsney had been interviewed by Krakauer, and maintained that Krakauer either misquoted or misunderstood what he said.
As a response to Krakauer's allegations, CAI produced a comprehensive list of projects completed over a period of years and projects CAI is currently working on. The list was released in December, 2011 (see external links below).
In May 2011, Jean Price and Michele Reinhart, Democratic Party representatives in Montana, along with Dan Donovan, a Great Falls attorney, filed a class action lawsuit against Mortenson and are asking a federal judge in Missoula to place all proceeds from the purchases of Mortenson's books into a trust to be used for humanitarian purposes. The total of Mortenson's book sales to date stand at near $5 million. In June 2011, Jean Price announced she was dropping out of the suit, explaining that she had never read the book. In Illinois, former school teacher Deborah Netter, also dropped her Illinois lawsuit against Mortenson in early July 2011, joining the Montana lawsuit in mid-July. The Montana lawsuit was subsequently dismissed on April 30, 2012. In October 2013, a class-action lawsuit claiming damages against Greg Mortenson over "Three Cups of Tea" was rejected by the 9th Circuit Court of Appeals.