Deputy Prime Minister Nick Clegg gave his consent to cabinet secretary Sir Jeremy Heywood to request the destruction of data files at The Guardian.
Clegg’s spokesman said he supported the move, as opposed to beginning legal proceedings, as he was “keen to protect” the paper’s freedom to publish while protecting national security.
Last night, it emerged that Heywood was directed by Prime Minister David Cameron to make contact with The Guardian about the classified material handed over by whistleblower Edward Snowden which provided the basis for a series of stories this summer outlining the extent of US surveillance operations.
Clegg is said to have agreed on the understanding that destroying the material would not affect The Guardian’s ability to continue to publish stories.
Clegg’s spokesman said: “We understand the concerns about recent events, particularly around issues of freedom of the press and civil liberties. The independent reviewer of terrorism legislation is already looking into the circumstances around the detention of David Miranda and we will wait to see his findings.
"On the specific issue of records held by The Guardian, the Deputy Prime Minister thought it was reasonable for the cabinet secretary to request that The Guardian destroyed data that would represent a serious threat to national security if it was to fall into the wrong hands.
"The Deputy Prime Minister felt this was a preferable approach to taking legal action. He was keen to protect The Guardian's freedom to publish, whilst taking the necessary steps to safeguard security.
"It was agreed to on the understanding that the purpose of the destruction of the material would not impinge on The Guardian's ability to publish articles about the issue, but would help as a precautionary measure to protect lives and security.”
Earlier this week, Guardian editor Alan Rusbridger reported that he had come under pressure to hand over the material leaked to the paper by Snowden. He said that a “very senior government official” had requested that the paper return or destroy documentation it held relating to the National Security Agency (NSA).
The paper agreed to destroy two hard drives in the presence of security officials, but Rusbridger said it had been a “pointless piece of symbolism” because The Guardian would continue to report on the story from abroad, where copies of the files existed.
He said he had agreed to the destruction of material to appease demands from Whitehall and curtail threats of legal action that could hinder the paper’s ability to report on the NSA leaks.
Former foreign secretary Sir Malcolm Rifkind, who chairs Parliament’s Intelligence and Security Committee, told BBC Radio 4’s Today programme that he supported the destruction of the material.
"I think Mr Rusbridger, in the article he wrote about the destruction of his hard disks, is on relatively weak ground,” he said. “He clearly did not dispute that he had no legal right to possess the files or the documents. The question was whether he handed them back to the government or whether they were destroyed. He chose the latter option.
"Clearly if he thought that what he was doing was perfectly lawful, that he was perfectly entitled to have these documents, he would have told the cabinet secretary – or whoever it was – to go and get lost and take me to court. But he didn't do that. He knew perfectly well that if you have in your possession documents which were originally stolen you are on pretty dodgy ground."
The news of the destruction of The Guardian’s files emerged in the aftermath of the detention of David Miranda, husband of Glenn Greenwald, the Guardian journalist who unveiled Snowden’s leaks, at Heathrow airport on Sunday on anti-terror laws.
Miranda was travelling to Rio from Berlin, where he had met Laura Poitras, the US film-maker who has been working with Greenwald and The Guardian on the NSA leaks.
He was held for nine hours under Schedule 7 of the Terrorism Act 2000, with reports suggesting he may have been asked to carry material relating to Snowden’s leaks. Rifkind agreed that use of anti-terror laws was a “sensitive issue” but insisted that national security should remain of paramount concern.
He said: “This was not about embarrassment to the government. The documents which Snowden stole from the National Security Agency are documents some of which deal with how the intelligence agencies get access to terrorist information through interception of mail or phone messages. That is something potentially relevant to terrorists and therefore it is not a question of embarrassment to the government."
Home Secretary Theresa May confirmed yesterday that she had been briefed in advance about the possible detention of Miranda and a spokesman said No 10 was "kept abreast of the operation in the usual way". It is understood that Clegg was not notified in advance.
May told the BBC: "If it is believed that somebody has in their possession highly-sensitive stolen information which could help terrorists, which could lead to a loss of lives, then it is right that the police act and that is what the law enables them to do."
But the Home Secretary, who has come under pressure to explain how much the Government knew about the planned detention of Miranda after the White House said it had been given a "heads up", said there were safeguards in place to make sure such arrests were conducted properly.
"I was briefed in advance that there was a possibility of a port stop of the sort that took place," she said.
"But we live in a country where those decisions as to whether to stop somebody or arrest somebody are not for me as Home Secretary, they are for the police to take. That's absolutely right that they have their operational independence and long may that continue."