The police moved in after protesters ignored Turkish Prime Minister Recep Tayyip Erdogan's demand to end the demonstrations.
Erdogan is reportedly due to meet with public figures over the issue which initially sparked the protests: a demonstration against the redevelopment project in Gezi Park, one of Istanbul's last urban green spaces.
Taksim Square is now strewn with wreckage from bulldozed barricades and remains largely deserted.
Officials said Monday that Erdogan had agreed to meet representatives of a group opposing the Gezi Park redevelopment plan.
Erdogan warned Tuesday that he would not show "any more tolerance" for those he accused of seeking to harm Turkey, the BBC wrote.
"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," he said.
Germany Foreign Minister Guido Westerwelle said Erdogan's government was sending the wrong signal both domestically and internationally with its reaction to the demonstrations.
"We expect Prime Minister Erdogan to deescalate the situation, in the spirit of European values, and to seek a constructive exchange and peaceful dialogue," Westerwelle said, describing the scenes of clashes in Taksim Square as "disturbing."
The protesters in Turkey have accused Erdogan of harsh and autocratic rule, which he denies.
The Irish Times quoted Erdogan's response to accusations on Tuesday:
“They say the prime minister is rough. So what was going to happen here? Were we going to kneel down in front of these [people]? If you call this roughness, I’m sorry, but this Tayyip Erdogan won’t change.”
Protesters also claimed his government was trying to impose conservative Islamic values on a secular state.
More than 50 lawyers had reportedly been detained for supporting the demonstrations.
Turkey’s Medical Association said almost 5,000 people had sought treatment for injuries since the unrest began, while three people had died.