Robert Litt, the general counsel to the Office of the Director of National Intelligence, has written to the New York Times to deny the allegation that James Clapper, the director of national intelligence, lied to Congress about the collection of bulk phone records by the National Security Agency (NSA).

Citing an editorial entitled “Edward Snowden, Whistle-Blower” which was published on Thursday, Litt wrote that the newspaper “repeats the allegation that James R Clapper Jr … ‘lied’ to Congress about the collection of bulk telephony metadata” and added: “As a witness to the relevant events and a participant in them, I know that allegation is not true.”

The Times editorial called for Snowden, a former NSA contractor who leaked thousands of files on the agency’s surveillance practices to media outlets including the Guardian, to be offered “a plea bargain or some form of clemency that would allow him to return home”. It also listed a number of what it called “violations” which he had revealed.

Among such violations, the editorial said: “His leaks revealed that James Clapper Jr, the director of national intelligence, lied to Congress when testifying in March that the NSA was not collecting data on millions of Americans. (There has been no discussion of punishment for that lie.)”

In his letter to the newspaper, referring to one of the key Senate advocates of NSA reform, Litt continued: “Senator Ron Wyden asked about collection of information on Americans during a lengthy and wide-ranging hearing on an entirely different subject. While his staff provided the question the day before, Mr Clapper had not seen it. As a result, as Mr Clapper has explained, he was surprised by the question and focused his mind on the collection of the content of Americans’ communications. In that context, his answer was and is accurate.

“When we pointed out Mr Clapper’s mistake to him, he was surprised and distressed. I spoke with a staffer for Senator Wyden several days later and told him that although Mr Clapper recognized that his testimony was inaccurate, it could not be corrected publicly because the program involved was classified.”

Litt concluded: “This incident shows the difficulty of discussing classified information in an unclassified setting and the danger of inferring a person’s state of mind from extemporaneous answers given under pressure. Indeed, it would have been irrational for Mr. Clapper to lie at this hearing, since every member of the committee was already aware of the program.”

Snowden is now in Russia, where he was given one year’s asylum. In the US, he faces charges of espionage and theft. In December Richard Ledgett, the NSA official in charge of assessing the damage caused by Snowden’s leaks, indicated that he was open to the possibility of an amnesty.

The White House dismissed that suggestion, President Barack Obama’s spokesman, Jay Carney, telling reporters: “Mr Snowden has been accused of leaking classified information and he faces felony charges in the US. He should be returned to the United States as soon as possible, where he will be accorded full due process.”