Nick Clegg has confirmed reports that top civil servant Sir Jeremy Heywood was sent to warn The Guardian to destroy classified data it had received from NSA whistleblower Edward Snowden.
On Wednesday his spokesman said the deputy prime minister was "keen to protect" the newspaper's freedom to publish while safeguarding national security.
Clegg agreed to the move on the understanding that destruction of the material would not impinge on The Guardian's ability to publish articles, he added.
It emerged last night that cabinet secretary Sir Jeremy was directed by prime minister David Cameron, backed by Clegg, to contact the Guardian about classified material handed over by Edward Snowden.
A spokesman for the deputy prime minster 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."
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 a series of security services exposes.
Scotland Yard and the Home Office have insisted the actions of officers at the airport were proper.
Home secretary Theresa May confirmed yesterday 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". It is understood Mr 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."
Miranda was detained at Heathrow Airport under Schedule 7 of the Terrorism Act 2000 as he changed planes on a journey from Berlin to his home in Brazil.
He claimed he was held for nine hours by agents, who questioned him about his "entire life" and took his "computer, video game, mobile phone, my memory card - everything".
Schedule 7 applies only at airports, ports and border areas, allowing officers to stop, search, question and detain individuals.
Its use has been criticised by Greenwald - the reporter who interviewed Snowden - as a "profound attack on press freedoms and the news-gathering process", and has sparked concern on the use of terror laws.
Lawyers for Miranda have written to both May and Britain's most senior police officer challenging the legality of the decision to detain him for nine hours using Schedule 7.
Law firm Bindmans said it has sent a letter to May and to Met Police commissioner Sir Bernard Hogan-Howe asking for explanation of who requested, and for what purpose, police to seize sensitive journalistic material from him.
They have also demanded assurances that none of the material will be disclosed or shared or used and, if guarantees are not given, will apply for an injunction, the company said.
Labour's Keith Vaz, chairman of the Home Affairs Select Committee, called on Cameron to make a "full statement" to Parliament on the day it returns after the summer break to explain his actions.
He said: "The actions of the Cabinet Secretary are unprecedented and show that this issue has reached the highest levels of government.
"Although I am very surprised at this revelation, it explains why Downing Street, the White House and the Home Secretary were briefed in advance about David Miranda's detention.
"Up until now, the UK Government has downplayed its interest in these matters but it's clear that they have taken a proactive stance, not just in terms of the destruction of the information held by the Guardian but also the involvement of those journalists who have written about Edward Snowden.
"The Prime Minister must make a full statement to Parliament on the day it returns. We need to know the full facts. Nothing less will do."