The Guardian deputy editor Paul Johnson has clarified his statement at a radio conference in Dublin that the British Government would close down the newspaper over the Edward Snowden spying affair.

Mr Johnson was asked on Tuesday at the Radiodays conference what specific threats were made by the British Government if they were to publish Mr Snowden’s revelations of mass surveillance by US and UK security agencies.

Mr Johnson responded: “Yes, we were being threatened with being closed down.”

When pressed as to if that meant the closure of the newspaper, he added: “Well there are specific threats made and there have been specific threats made legally. We didn’t know if they were under the terror laws or the more ordinary laws about the seizure of journalistic material.”

He then played a video to show how the newspaper dealt with the threat.

He has since contacted The Irish Times to state that he meant to convey that the British Government would close down its coverage of the Snowden leaks, rather than the newspaper itself.

Mr Snowden is now in Russia, where he has temporary asylum. He is wanted by the US authorities on espionage charges.

He has been responsible for one of the biggest intelligence leaks of all time, using his access to data systems to reveal the extent to which British and US agencies were spying on ordinary citizens and world leaders including German chancellor Angela Merkel.

Speaking at the Conference Centre Dublin (CCD) on Tuesday, Mr Johnson, who was in charge of handling the Snowden material, said it was much more difficult to work on than the WikiLeaks tapes because of the intense scrutiny the newspaper was subjected to by the British intelligence services.

As a contractor working for the NSA, Mr Snowden had access to an enormous amount of classified information.

However, Mr Johnson said he had been told by a senior British government official that 850,000 Americans had the same level of access to classified information as Mr Snowden.

The Guardian became involved with Mr Snowden because of the work the newspaper did in relation to WikiLeaks and the phone hacking at the News of the World .

Mr Johnson told the conference: “It was the most difficult story we have ever done and that includes WikiLeaks, because reporters and editors couldn’t speak to each other. We could only speak using encryption systems.”

The Guardian set up a secure room and used new computers that had no outside access to the internet, with a guard outside the door all the time.

Mr Johnson revealed that a senior civil servant had told the paper’s editor, Alan Rusbridger, that the “prime minister, the deputy prime minister, the foreign secretary, the home secretary and the attorney general have got a problem with you”.

Mr Johnson said the whole attitude in the UK was that national security trumped press freedom and that the newspaper should not publish a word. This was in contrast to the US, where the Snowden revelations had led to a debate about how far intelligence agencies should go to protect the state.

“We were accused of endangering national security and people’s lives. It left us in a very difficult position,” he said.