Police moved in on protesters who were still camped on the square following bigger demonstrations on Friday night against President Viktor Yanukovich's decision not to sign a landmark agreement on trade with the European Union.
Yanukovich, in a statement to the Ukrainian people posted on his website later Saturday, said he was "deeply outraged" by incidents and called for an immediate and objective investigation so that those guilty could be punished. He did not specifically blame the police for the incidents.
Witnesses said police first fired stun grenades at the crowds and then moved in, using batons to disperse them, chasing some protesters into nearby streets.
At 5 am on Saturday, part of the square was sealed off by black-helmeted riot police. Nine years earlier, the square had been the scene of the Orange Revolution protests against misconduct and electoral fraud.
Tension had been building in Kiev since Friday, when Yanukovich walked away from signing the pact with EU leaders at a summit in Lithuania, going back on a pledge to work toward integrating his ex-Soviet republic into the European mainstream.
He said the cost of upgrading the economy to meet EU standards was too great and added that economic dialogue with Russia, Ukraine's former Soviet master, would be revived.
On Friday night, at least four people were beaten by police, including a Reuters cameraman and a Reuters photographer, who was bloodied by blows to the head by police.
The Interfax news agency reported that police had decided to clear Independence Square after "a number of incidents".
In the Friday night demonstrations, which involved about 10,000 protesters, heavyweight boxing-champion-turned-politician Vitaly Klitschko said Yanukovich had dashed the aspirations of Ukrainians to join mainstream Europe.
"Today they stole our dream, our dream of living in a normal country," said Klitschko, a contender for the 2015 presidential election. "The failure to sign the agreement of association is treason," he said.