Risen and Eric Lichtblau were awarded the Pulitzer Prize for National Reporting in 2006 for a series of controversial investigative reports that they co-wrote about the National Security Agency's surveillance of international communications originating or terminating in the United States and about a government program called Terrorist Finance Tracking Program designed to detect terrorist financiers, which involved searches of money transfer records in the international SWIFT database.[citation needed]

The White House Press Office issued a statement on August 6, 2007 that the New York Times article on the Congressional and Presidential approval of a six-month extension of terrorism monitoring in the United States was misleading.[citation needed]

Risen is the author of the book State of War: The Secret History of the CIA and the Bush Administration (January 2006). The book makes numerous controversial allegations about Central Intelligence Agency activities. It alleges that the CIA carried out an operation in 2000 (Operation Merlin) intended to delay Iran's nuclear weapons program by feeding it flawed blueprints for key missing components - which backfired and may actually have aided Iran, as the flaw was likely detected and corrected by a former Soviet nuclear scientist the operation used to make the delivery.

The CIA Public Affairs Office issued a press release indicating that Risen's book contains serious errors in every chapter.

Risen writes in State of War that, "Several of the Iranian [CIA] agents were arrested and jailed, while the fate of some of the others is still unknown", after a CIA official in 2004 sent an Iranian agent an encrypted electronic message, mistakenly including data that could potentially identify "virtually every spy the CIA had inside Iran". The Iranian was a double agent and handed over the information to Iranian intelligence. This also has been denied by an intelligence official. Risen also alleges that the Bush Administration is responsible for transformation of Afghanistan into a "narco-state", that provides a purported 80% of the world's heroin supply.

The publication of this book was expedited following the December 16, 2005 NSA leak story. The timing of The New York Times story after the Iraq election in mid December 2005 is a source of controversy since the story was delayed for over a year. The New York Times story appeared two days before a former NSA employee, dismissed in May 2005, requested permission to testify to two Congressional intelligence oversight committees. Byron Calame, the Public Editor of The New York Times, wrote in early January 2006 that two senior Times officials refused to comment on the timing of the article.

Risen says this book is based on information from a variety of anonymous sources, and he is scheduled to appear before a Grand Jury in February, 2008, on sources of allegations of CIA operations. The Department of Justice (DOJ) conducted an investigation of the sources of the security leak involving the NSA. These follow an earlier investigation of the Valerie Plame leak that resulted in former New York Times reporter Judith Miller being jailed before she agreed to reveal her source. The Attorney General hinted in a Washington Post article on May 22, 2006 that journalists may be charged for any disclosure of classified national security information. President George W. Bush, in a June 25, 2006 news conference, was critical of the publication of information of classified programs by the New York Times. Risen was subpoenaed in 2008.

In an article that Risen cowrote with Jeff Gerth for The New York Times in 1999, they allege that "a Los Alamos computer scientist who is Chinese-American" had stolen nuclear secrets for China.[citation needed]

The suspect, later identified as Wen Ho Lee, pled guilty to a single charge of improper handling of classified data, the 58 other counts against him were dropped, and he was released from jail . No espionage charges were brought or proven.[citation needed]

Later , the New York Times apologized for significant errors in reporting of the case.[citation needed] It was one of five newspapers, including also the Los Angeles Times, which jointly agreed to pay damages to settle a lawsuit concerning their coverage of the case.