Police in the eastern Siberian region of Buryatia said they had detained the shaman, Alexander Gabyshev, on a highway near Lake Baikal and would send him back to his home region where he is "wanted for committing a crime".
Gabyshev's eccentric bid to walk from his home city of Yakutsk to Moscow, a distance of some 5,000 kilometres (3,000 miles), has seen a group of followers join him on the way.
His simply expressed statements about Putin captured public attention, prompting opposition protests as well as a sharp response from the authorities and muck-raking reports on pro-Kremlin television.
Opposition leader Alexei Navalny has mocked the official reaction to the shaman as showing the Kremlin's paranoia about any sign of dissent.
"Putin is scared. He's already stomping his feet and shouting: "God save me from this shaman. What if he really does banish me?" Navalny said in a video blog on September 14.
When the long-haired self-proclaimed shaman reached the Siberian city of Ulan-Ude in August, he was accosted by a group of rival shamans who ordered him not to enter the city. Clashes ensued and several of those accompanying Gabyshev were detained.
Heated opposition protests began early this month in Ulan-Ude with pickets in support of the detained followers of the shaman, but also reacting to alleged falsification of local elections. Riot police roughly broke up protests and detained and charged leading figures.
Previously in July in the Siberian city of Chita, Gabyshev spoke at a rally with hundreds attending wearing a Che Guevara T-shirt.
Gabyshev began walking in March. He planned to reach Moscow in 2021.
Shamanism is still practised in numerous regions of Russia.