Harding's expulsion follows his coverage of the WikiLeaks US embassy cables release for the Guardian, in which he said the country was being run like a a "virtual mafia state".
He tweeted last night: "The Russians have been unhappy with my reporting for a while. But it seems WikiLeaks may have been the final straw."
Harding was attempting to re-enter Russia at the weekend after a two-month stint in London working on the newspaper's cables coverage.
According to a statement from the Guardian, he was stopped at the airport and detained in a cell for 45 minutes. He was then reportedly placed on a return flight and told, "For you, Russia is closed."
Harding tweeted that he was "extremely sad to leave Russia under these circumstances. My visa valid until end of May."
Alan Rusbridger, editor-in-chief of Guardian News & Media, said: "This is clearly a very troubling development with serious implications for press freedom, and it is worrying that the Russian government should now kick out reporters of whom they disapprove.
"Russia's treatment of journalists - both domestic and foreign - is a cause of great concern. We are attempting to establish further details, and are in contact with the Foreign Office."
In a statement released yesterday, the Foreign Office said that it was trying to communicate with its Russian counterparts over the issue.
"We have been in contact with the Russian Ministry of Foreign Affairs, including through a call from the Foreign Secretary, to seek clarity on this decision. We are awaiting a reply."
International Federation of Journalists general secretary Aidan White said the expulsion would "worry campaigners for press rights inside Russia and across the globe".
"This expulsion is a chilling reminder of how easy it is for the current Russian leadership to slip back into the shadows of censorship of years past," he said in a statement.
"[It] shows that political intolerance of independent journalism is growing. It should be condemned by all those campaigning for democratic rights in the country and beyond."
Harding has spent more than a decade covering foreign affairs for the Guardian - with postings in New Delhi, Berlin and Russia - and has reported from Afghanistan, Iraq and other conflict zones.
He is co-author of the newspaper's recent book, WikiLeaks, Inside Julian Assange's War on Secrecy, with Guardian investigations editor, David Leigh.
Russia's Foreign Ministry issued a statement yesterday apparently reversing the decision to deport Harding, claiming that he "will not experience any problems with entering the Russian Federation" and blaming administrative errors by Harding for the situation.
"The explanation is that he has committed a whole series of breaches of the rules governing the work of foreign correspondents, as approved by the government of the Russian Federation and which are well known to all journalists.
"In particular, after requesting and receiving an extension to his accreditation in late November of last year, Harding left Moscow for London to attend to his own matters, without obtaining the foreign correspondent identification papers that had been issued for him, even though he was aware of the need to do so."
Guardian News & Media responded to the statement last night, discrediting the claim that an administrative error was at fault."We are baffled by the statement issued by the Russian foreign ministry today. We have still not received an adequate explanation of why Luke Harding was deported on arrival at Moscow airport on Saturday February 5th, despite having a valid visa.
"Failure to collect his press card before leaving urgently on a trip to London is manifestly not a plausible reason for detaining Luke at the airport and refusing him entry to Russia.
"This is part of a pattern of behaviour by the Russian foreign ministry who first expelled Luke Harding in November 2010. That expulsion was partially delayed after intervention by the British government, but it was understood that Luke would have to leave by May 2011.
"We did not make this public at the time but it discredits attempts to portray this week's expulsion as an administrative error."
The Guardian issued a further statement on 10 February stating that it welcomed the offer from the Russian Foreign Ministry to give Harding a new visa.
"Luke and the Guardian are now considering the offer very carefully."
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