The Deputy Prime Minister was “keen to protect” the newspaper’s freedom to publish while safeguarding national security, his spokesman said.
Mr Clegg agreed to the move on the understanding that destruction of the material would not impinge on the paper’s ability to publish articles, he added.
It emerged yesterday that Cabinet Secretary Sir Jeremy was directed by Prime Minister David Cameron, backed by Mr Clegg, to contact the Guardian about classified material handed over by whistleblower Edward Snowden.
A spokesman for the deputy prime minister 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 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.”
The intervention ordered by No 10 came to light following the detention at Heathrow Airport under terror laws of David Miranda, partner of Guardian journalist Glenn Greenwald who has worked with Snowden on security services exposés.
Scotland Yard and the Home Office have insisted the actions of officers at the airport were proper.
Home Secretary Theresa May confirmed on Tuesday that she had been briefed in advance about the possible detention of Mr Miranda and a spokesman said No 10 was “kept abreast of the operation in the usual way”.
Mrs May said: “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 Mr Miranda after the White House revealed 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.”
Rifkind warns leaked data will help terrorists
REPORTS using information obtained by US whistleblower Edward Snowden will have played into terrorist hands, a former foreign secretary has said.
Sir Malcolm Rifkind criticised Guardian newspaper editor Alan Rusbridger, who he said was on “weak ground” and in no position to judge whether leaked information posed a national security threat.
He said: “There’s no question that the various press reports of some of the Snowden leaks – what Snowden has given to various newspapers in the United States and the United Kingdom – gave information about the way in which intelligence agencies are able to access e-mails or telephone calls by people who they suspect are terrorists – procedures that are much more sophisticated than perhaps terrorists understood.”