Local media reported that between 100 and 200 people were detained, but the authorities declined to confirm the figure.
Second-hand cars are popular in Russia's far east, where second-hand Japanese vehicles are regularly brought in.
Further protests were due to take place across Russia on Sunday, with political analysts saying they indicate the first serious challenge to measures being taken to fight a financial downturn.
The global economic crisis has battered Russian financial markets. Oil, a chief source of foreign currency revenue, has fallen from $147 to under $40 a barrel in the past six months.
Nikolai Kostalenko, a car dealer who took part in the protest, said: "For me, the car business is the only way to support my family."
Nikolai Markovtsev, a local parliamentarian with the pro-Kremlin Fair Russia party, said protesters want to protect their jobs.
"The government has shown how it interacts with the people. They should talk to people, not twist their arms," he said.
The car duty is largely a defensive measure to protect Russia's domestic motor industry, which is based around the Volga region in cities such as Togliatti, home of the Soviet-era Lada.