The Guardian newspaper, however, said it was "baffled" by the statement and hadn't received an adequate explanation of why Moscow-based Luke Harding was refused entry to the country when he tried to fly in from Britain on Saturday.
The incident raised the prospects of a new flare-up of tensions between Moscow and London.
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 on Tuesday 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."
Harding had been in Britain since November working on a book about WikiLeaks. The Guardian said he was held in a Moscow airport detention cell for about 45 minutes Saturday, then put on a London-bound plane and given back his passport with his Russian visa canceled.
The Russian Foreign Ministry said Harding was refused entry because he had committed violations of accreditation rules "which are well known to all journalists." However it specified only one - the failure to obtain a new accreditation card before leaving the country.
The ministry statement said if Harding resolves the accreditation issue, he can return to work in Russia for the period of his current visa. However, if his visa - which is separate from government accreditation as a journalist - was revoked as the newspaper has reported, he could face additional bureaucratic obstacles.
Foreign Minister Sergey Lavrov was quoted by the state news agency RIA Novosti as saying "nobody annulled his visa."
Harding previously had been detained in April 2010 in Ingushetia, one of the Russian Caucasus republics where security forces are fighting an Islamic insurgency.
"We warned him that he had several times broken regulations," Lavrov said Tuesday. "He more than once visited a zone that was under a counterterrorism regime and was informed by security services that he was obliged to make this known."
British Foreign Minister William Hague plans to discuss the issue with Lavrov in a meeting in London next week. Some British lawmakers suspect Harding was targeted after he wrote a Dec. 1 article quoting U.S. diplomatic cables leaked by WikiLeaks that described Russia as a corrupt autocracy.
The Guardian took strong issue with Russia's account.
"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 ... despite having a valid visa," the paper said.
The paper said Russian authorities first expelled Harding in November 2010, an expulsion that was partially delayed after the British government intervened. It said Harding "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."
Lavrov said Harding's Russian visa had expired last fall but he was granted an extension "for family reasons."
Associated Press writers David Stringer and Sylvia Hui in London contributed to this report.