Ovdinfo, a rights group that tracks arrests at demonstrations, said 352 were detained at two anti-war protests in central Moscow.
Police gave a much lower figure of 50 people detained for "attempts to violate public order", the Interfax news agency said.
Anti-war protesters gathered near the defence ministry in central Moscow and on Manezhnaya square close to the Kremlin.
Demonstrators held up peace signs and posters saying "No to war", while some also held Ukrainian flags and ribbons in the national colours of yellow and light blue.
Many people brought to police stations were accused of resisting police orders, which could carry up to 15 days in jail, Ovdinfo said.
Dozens were also detained in Saint-Petersburg, after some 500 people staged a protest, an AFP correspondent said.
Authorities meanwhile allowed rallies in several cities in support of Putin's policy on intervention, even closing central Moscow boulevards to traffic to allow a march.
Moscow police said 20,000 people took part in a pro-war march as television footage showed people walking with Russian flags as well as yellow-and-black nationalist flags and posters with slogans such as "Bravo Putin!"
The pro-Kremlin United Russia party posted an invitation to the demonstration on its website, saying Russian speakers were "faced with persecution and violence because they speak Russian and are friendly toward Russia."
Moscow police said that supporters of military intervention in Crimea also held a rally of about 50 cars called "We don't abandon our own people".
Russia's Federation Council, the upper house of parliament, on Saturday unanimously approved Putin's request to send Russian troops into Ukraine.
Lawmakers also said the Russian ambassador to the United States should be recalled.
Putin said Russia needs to protect the lives of Russian citizens in regions close to Russia and servicemen from its Black Sea fleet after a pro-Western opposition movement deposed Ukraine's President Viktor Yanukovych.
Kiev accused Russia of covertly invading the Crimean peninsula on Saturday, when armed men occupied several government buildings and the airport and installed checkpoints on the peninsula.