They were calling on the federal authorities to dismiss Murtaza Rakhimov from his post as president of Bashkortostan. The authoritarian Rakhimov has ruled this Muslim-majority republic in the South Ural mountains since 1993.
One of the protesters held a placard reading "Rakhimov's regime is arbitrary, corrupt, and violent.” A handful wore striped uniforms supposed to represent those worn by prisoners in Nazi concentration camps.
Airat Dilmukhametov is the leader of the Bashkir National Front, one of the republic's more radical opposition movements. He says Rakhimov has presided over a dictatorship where human rights are regularly violated.
"Over the past 15 years there have been many cases of death, murder, poisoning, car crashes, torture, illegal punishment," Dilmukhametov said. "A dictatorship has been established [in Bashkortostan]. This is why people are disappointed and many of them are scared."
The Bashkir opposition also accuses Rakhimov of corruption. It charges that the oil companies controlled by Rakhimov's son, Ural, have mismanaged millions of dollars through tax evasion.
The demands of the Bashkir opposition, however, are likely to fall on deaf ears.
Dilmukhametov says he has little hope that Rakhimov, who was reelected president in 2003 with the support of Russian President Vladimir Putin, will be sacked. The Kremlin is widely regarded as turning a blind eye to Rakhimov's alleged abuses in return for his loyalty.
Unrest in Bashkortostan has been growing since police detained and injured several hundred people in a violent sweep of the town of Blagoveshchensk in December 2004.
Rights groups say over 1,000 men were arrested and taken to police stations, where they were reportedly beaten and humiliated.
Dilmukhametov hopes the recent protest will draw Moscow's attention to the republic's problems in the face of growing unrest.
"We are doing this [protesting] in order for our conscience to be clear in case the situation in Bashkortostan takes a different turn," Dilmukhametov said. "We are now warning the public and the federal leadership. This is one of our last warnings."
Dilmukhametov says the opposition movement in his republic was inspired by the recent mass protests that recently toppled the government in Ukraine and Kyrgyzstan.
Boris Kagarlitsky, a political analyst who heads Moscow's Institute for Globalization Studies, believes the Russian authorities will ignore the protest. But he argues that Bashkortostan's government is not viable and that the crisis could eventually destabilize the Kremlin.
“If you don’t sacrifice Rakhimov, if you do not react to the demands of the opposition, which I think is going to be the case, then the movement will radicalize," says Kagarlitsky. "From being a movement against a local leader it will become a movement against Moscow as well."
According to the Bashkir opposition, Rakhimov's government has spared no effort to try to sabotage the protest.
Opposition leaders were delayed for five hours on Thursday after additional security checks at the airport in Ufa, the capital of Bashkortostan. The oppositionists say the checks were ordered by the Bashkir government.
They say airport officials also tried to confiscate boxes containing the lists of over 150,000 signatures in support of Rakhimov's dismissal. The boxes were later delivered to Putin's administration by the protesters in Moscow.
The Bashkir government was swift to fend off the allegations and branded the protest an attempt at undermining it.