Foreign Office Minister David Lidington says the government "deplores" Russia's expulsion of a British journalist working for the Guardian newspaper.
Luke Harding, who reported on Wikileaks cables containing criticism of Russia's leadership, was refused permission to re-enter the country at the weekend.
He had reported on US cables describing Russia as a "virtual mafia state".
Moscow's foreign ministry has said he had broken media rules but could be re-admitted to the country.
It said this may be allowed if he fixes his press accreditation problems by contacting the Russian Ministry of Foreign Affairs' information and press department.
Mr Lidington said the Foreign Secretary, William Hague, would be raising the matter with the Russian Foreign Minister, Sergei Lavrov, when he visits Britain next week.
A Guardian article reported that Mr Harding was stopped from re-entering Russia at the weekend and sent back to the UK.
Mr Harding wrote on his Twitter page: "Russia has expelled me from Moscow. Stopped at pass control, put in a locked cell and deported. No explanation given."
The Guardian reported his visa was annulled and a security official told him, "for you Russia is closed".
'Meticulous and courageous'
Labour MP Chris Bryant, a former Foreign Office Minister, tabled a question in Parliament about Mr Harding and said the reporter's British wife and young children were "stuck in Russia without him".
Mr Lidington said: "Mr Harding is a journalist who knows Russia well and has given readers of the Guardian a genuine insight into that country.
"A free media and freedom of expression is a vital element of any free and democratic society and the government deplores any restriction on those freedoms."
The minister said Mr Hague had spoken to Mr Lavrov about Mr Harding's case and the Russian government was making inquiries.
Mr Harding's wife would be offered consular assistance, he said, adding: "We are unafraid to raise matters [with Russia] on which we disagree."
Mr Bryant described Mr Harding as a "meticulous and courageous" journalist and said the attempt to silence him echoed the harassment of other reporters in Russia, including Anna Politkovskaya, who was murdered in 2006.
He said the affair smacked of the "worst practices of the Communist era".
Mr Bryant added: "Those who have heard Russia described as a mafia state or a kleptocracy might think that this is not far off the mark."
'Observe the rules'
In a statement on its website, the Russian Ministry of Foreign Affairs' information and press department said Mr Harding had "committed a whole series of breaches of the rules" governing the work of foreign correspondents.
"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," it said.
If he wanted to keep working in Russia he needed to resolve this issue by contacting the department, it continued.
"Provided that he observes these rules, which are the same for all foreign correspondents, Harding will not experience any problems with entering the Russian Federation."
A Guardian spokeswoman said they were "baffled" by the Russian statement.
"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," she said.
She said the expulsion was part of a "pattern of behaviour" by the Russians.
The chairman of the Russian Union of Journalists, Vsevolod Bogdanov, criticised the decision and said: "I have very hard feelings about what happened. The Guardian has great authority in the world and its journalists work according to the code of ethics and preserve their reputation.
"That is why I do not like all this," Bogdanov told the Russian Interfax news agency.
There have been tensions between the UK and Russia since the 2006 murder of Kremlin critic Alexander Litvinenko in London.
In December, a diplomat was expelled from Russia's embassy in London for espionage and Russia responded in kind.