He flew from Berlin to Moscow, arriving in Russia for the first time since he was nearly killed by a nerve agent attack.
The activist says the authorities were behind the attempt on his life, an allegation backed up by investigative journalists but denied by the Kremlin.
Russia's FSIN prison authority confirmed that officers had detained him, the Interfax news agency reported.
Metal barriers were erected inside the airport, Vnukovo, and Russian media reported that several activists - including key Navalny ally Lyubov Sobol - had been detained there.