Eduard Limonov, one of the leaders of the The Other Russia, was among those arrested, his spokesman said.
As protesters began to leave, police formed a corridor leading to the subway station and beat or detained all those attempting to break out.
A middle-aged woman was left with a bloody nose.
Police rushed to kick a man as he lay on the ground after falling from a fence he had tried to climb to escape the cordon.
On Saturday in Moscow, 9,000 riot police and soldiers were deployed to prevent less than 2,000 Other Russia activists marching to a central square.
Police arrested some 200 protesters including Garry Kasparov, one of Other Russia's leaders and the former world chess champion.
He was released after being fined the equivalent of $40.
"It is no longer a country ... where the government tries to pretend it is playing by the letter and spirit of the law," Kasparov said outside the court building.
"We now stand somewhere between Belarus and Zimbabwe," he said.
Tensions are rising ahead of the March 2008 presidential election to replace Putin, who is constitutionally required to step down at the end of his second term.
Putin, who has overseen rapid economic growth in Russia, is popular and analysts believe that whoever the former KGB officer endorses as his successor will face little opposition.
Opponents say that overwhelming dominance is the result of a powerful state media machine, an economic bonanza from high world oil prices, and the growing power of the security forces.