Interior Minister Muammer Guler said more than 1,700 people had been arrested in the unrest that has spread to 67 cities nationwide, though most have since been released.
In Istanbul, a sea of protesters from across Turkey's political spectrum flooded Taksim a day after police pulled out of the area, waving flags and chanting "Government, Resign!" and "Istanbul is ours, Taksim is ours!".
Taksim has been at the heart of a wave of protests that have spread across the country in the biggest public outcry against Prime Minister Recep Tayyip Erdogan's government since it took power in 2002.
The unrest began as a local outcry against plans to redevelop Gezi Park near Taksim, but after a heavy-handed police response quickly snowballed into broader protests against what critics say is the government's increasingly conservative and authoritarian agenda.
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After two days of violence, the situation appeared to have calmed in Istanbul today after police pulled out of Taksim and officials adopted a more conciliatory tone.
But in Ankara police fired tear gas and used water cannon to disperse some 1,000 protesters who were attempting to march on the prime minister's high-security office.
Authorities say almost 100 police vehicles, 94 shops and dozens of cars have been damaged.
"They call me a dictator," Erdogan said in a speech today. "If they liken a humble servant to a dictator, then I am at a loss for words."
He had insisted yesterday that his government would press ahead with the controversial redevelopment near Taksim although he said the project may not include a shopping mall, as feared by protesters.