LifeNews, a tabloid-style news site believed to have close ties to the Kremlin and Russian security services, said its office in Moscow was searched by federal investigators on March 24.
LifeNews said on its website that officers of the Investigative Committee confiscated documents.
Activists say office searches by law enforcement agents are a common form of pressure on organizations that oppose or criticize the Kremlin, but LifeNews is an unexpected target because it is seen as loyal to President Vladimir Putin.
The search is likely to fuel further speculation about infighting in Russia's ruling structure following the assassination of opposition politician Boris Nemtsov on February 27.
LIfeNews said the search was triggered by a complaint from a rights group, Soprotivleniye (Resistance), that suggested the news outlet's reports might have violated a law against publishing information revealing the identity of minors who are crime victims.
LifeNews said its reports did not violate the law.
According to Meduza, a Latvia-based news site that covers Russia, Soprotivleniye's head is the wife of a former Kremlin official.