Police detained more than 700 people, including over 300 in Moscow and nearly 150 in St Petersburg, according to OVD-Info, an independent website that monitors political arrests in Russia.
Some of the arrested individuals were minors, OVD-Info said.
The demonstrations followed protests that erupted within hours Wednesday after Putin, in a move to beef up his volunteer forces fighting in Ukraine, announced a call-up of experienced and skilled army reservists.
The defence ministry said about 300,000 people would be summoned to active duty, but the order left a door open to many more getting called into service.
Most Russian men ages 18-65 are automatically counted as reservists.
On Saturday, police deployed in force in the cities where protests were scheduled by opposition group Vesna and supporters of jailed opposition leader Alexei Navalny.
They moved quickly to arrest demonstrators, most of them young people, before they could hold protests.
In Moscow, a heavy contingent of police roamed a downtown area where a protest was planned and checked the IDs of passers-by. Officers rounded up those they deemed suspicious.
A young woman climbed on a bench and shouted "We aren't cannon fodder!" before police took her away.
In St Petersburg, small groups of demonstrators managed to gather and shout protest slogans before being rounded up.
In the city of Novosibirsk in eastern Siberia, over 70 people were detained after singing an innocuous Soviet-era song praising peace.
In another Siberian city, of Irkutsk, police handed summons to military conscription offices to men who took part in a protest.
People who tried to hold individual pickets that are allowed under Russian law also were detained.
The quick police action followed the dispersal of Wednesday's protests, when over 1300 people were detained on Wednesday in Moscow, St Petersburg and other cities.
Putin on Saturday signed a hastily approved bill that toughens the punishment for soldiers who disobey officers' orders, desert or surrender to the enemy.
