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.
Navalny - who had been treated in Germany - earlier appealed to supporters to meet him off the flight, and a "Let's meet Navalny" page has been set up on Facebook (in Russian). Thousands of people have said they will go or expressed an interest, despite forecasts of extreme cold.
After boarding his Pobeda airlines plane, the opposition politician said: "I'm sure that everything will be absolutely fine, I'm very happy today."
He also accused the Kremlin of encouraging people to go to Vnukovo to see a pop star, Olga Buzova, in a bid to squeeze out his supporters.
Navalny collapsed on an internal flight in Siberia last August, and it later emerged he had been poisoned with a Novichok nerve agent.
Russian authorities have consistently denied any role in the poisoning, and the Kremlin has rejected Mr Navalny's claims that President Vladimir Putin himself ordered it.
The Putin critic has said he misses Moscow, is almost fully recovered from the attack, and that there was never any doubt he would return.