Luke Harding's re-entry into Russia comes the same day a two-day visit to Britain by Russian Foreign Minister Sergei Lavrov begins, a trip meant to work on ties between the two countries.
Lavrov has said Harding violated accreditation rules but would be allowed to continue his work until May. The Guardian said the new media card provided by the Russian government when Harding returned Saturday expires on May 31.
"It is still not clear whether Luke is being allowed in indefinitely or is still being expelled in 15 weeks' time. The Guardian is seeking urgent clarification on this," the newspaper said in a statement.
Harding was initially informed in November that would have to leave when his media accreditation expired that month, and it would not be renewed, the Guardian said. However, when he tried to enter the country on Feb. 5, he was deported by security officials who told him "Russia is closed for you," the paper said.
Harding confirmed to The Associated Press late Sunday that he is back in Russia. He was in Britain from November to February working on a book about WikiLeaks.
Lavrov is expected to discuss Harding's case with his British counterpart William Hague and Prime Minister David Cameron.
Relations in recent years had been troubled by Britain's expulsion of alleged spies, by the murder in London of dissident former Russian security officer Alexander Litvinenko and by Britain's granting asylum to a Chechen rebel envoy and to billionaire Kremlin critic Boris Berezovsky.
Britain's Europe Minister David Liddington told the House of Commons last week that although Britain and Russia have many common interests, "it is also important that we are unafraid to raise very clearly in our discussions with Russian ministers and Russian officials those areas about which we disagree, and disagree strongly."