Nick Clegg approved plans ordering a top civil servant to call on the Guardian to destroy classified data in the interest of national security, according to his spokesman.
The Deputy Prime Minister was "keen to protect" the newspaper's freedom to publish but backed the move, ordered by David Cameron, because it was "preferable" to taking legal action.
Home Secretary Theresa May insisted asking Cabinet Secretary Sir Jeremy Heywood to contact The Guardian about classified material handed over by Edward Snowden was "right and proper".
But Labour's Keith Vaz said the actions were "unprecedented" and called on the Prime Minister to make a "full statement" to Parliament on the day it returns after the summer break.
"The actions of the Cabinet Secretary are unprecedented and show that this issue has reached the highest levels of government," the Home Affairs select committee chairman said.
"Up until now, the UK Government has downplayed its interest in these matters but it's clear 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 journalists who have written about Edward Snowden."
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 Mr Snowden on a series of security services exposes.
Scotland Yard and the Home Office insisted the actions of officers at the airport were proper.
A spokesman for the Deputy Prime Minster said: "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."
Foreign Secretary William Hague said: "The Government clearly has a duty if information is held insecurely and could be damaging to our national security to try to make sure that it is recovered or destroyed."