Tuesday's violence began with a dawn raid at the iconic square, which has seen demonstrators numbering in the tens of thousands in recent days; just a few hundred were camped out overnight.
Early-morning commuters scurried into cafes on the fringes of the square -- where they were offered lemon cubes to mitigate the effects of tear gas -- as hundreds of police officers backed by armored vehicles overran improvised barricades and moved into the area. Security forces fired volleys of tear gas and water cannons at the protesters and tore down posters that hung above the square.
A small group of protesters – scarves wrapped around their heads – hurled Molotov cocktails and aimed fireworks at police positioned under a revered statue in the center of Taksim Square. Others set ablaze a vehicle, sending plumes of smoke into the sky.
"To those who … are at Taksim and elsewhere taking part in the demonstrations with sincere feelings, I call on you to leave those places and to end these incidents, and I send you my love," Erdogan said in a televised address to members of parliament from his Justice and Development Party in the capital, Ankara.
"But for those who want to continue with the incidents I say: 'It's over.' As of now we have no tolerance for them," Erdogan was quoted as saying by the Associated Press. "Not only will we end the actions, we will be at the necks of the provocateurs and terrorists, and no one will get away with it."
The dawn raid came after several days of calm in the square in which protests -- initially demonstrations against the planned destruction of Gezi Park that morphed into an anti-government movement after a police crackdown -- began to resemble a festival. Reggae bands played in the area and thousands of young people camped out, eating, drinking and dancing.
The protesters are made up mostly of middle-class youth, born after the political violence that swept Turkey in the 1970s and largely unaffiliated with any political party. Instead, they represent a fiercely nationalistic and secular current and feel threatened by what they see as Erdogan's authoritarianism and the ruling party's increasing focus on Islamic strictures.
Violence has also flared in other cities around the country, notably in Izmir and Ankara. At least two protesters and one police officer have died in the clashes. A doctors union has reported more than 4,000 injured.
Officials initially said that Tuesday's raid was to remove posters from the statue in Taksim Square and the nearby Ataturk Cultural Center and would not affect demonstrators assembled in Gezi Park. However, Interior Minister Muammer Guler later said the "intervention took place to normalize life" at the square, state media reported.
Running battles between the two sides continued into the afternoon Tuesday. At one point, police began marching toward the park, but retreated after a brief confrontation with protesters, witnesses said.
"It was provocation," said one female protester, who asked to be referred to as Deniz A., standing in Gezi Park on Tuesday afternoon as tear gas hung in the air. "They want clashes with us, then they can portray us as the aggressors."
Erdogan defended the police operation, according to local media reports.
"What were we supposed to do? Kneel in front of these people and ask them to remove the banners? How would those illegal rags be removed from public buildings?"
Tuesday's raid came despite reports that negotiations between the Justice and Development Party, known as AKP, and the Gezi Park movement were set to commence. Erdogan is expected to meet with representatives of the protesters Wednesday.
On Sunday, Erdogan gave fiery speeches at six rallies across the country, scuttling hopes that he would strike a more conciliatory note. Despite scrapping plans to build a shopping mall in the park, he has shown few signs of relenting to protesters' demands. He insists that development in the area will go ahead, suggesting that a mosque or an opera house may be built.
"How can you attack my police? There are those who side with those swearing against the prime minister of this country. We are going to show patience, but patience has a limit as well," the Hurriyet Daily News quoted Erdogan as saying.
Senior AKP representatives have previously struck a more sympathetic note.
"The government is playing good cop, bad cop," said Bilgesu Ilgar, a student camped out in Gezi Park. "We need a completely new government. We cannot trust the AKP."
The AKP is planning to stage counter-rallies in Ankara and Istanbul later this week to marshal its support base.