The tear gas, water cannons and smoke grenades against the protesters came hours after Istanbul's police chief said his force would use tear gas only as a last resort.
It also followed a partial apology by Deputy Prime Minister Bulent Arinc for police brutality that sparked the nationwide unrest.
Arinc called the crackdown on demonstrators that led to days of nationwide protests "wrong and unjust."
He said his conciliatory remarks were addressed to environmentalists who staged a peaceful sit-in May 28 to save Istanbul's small, tree-lined Taksim Gezi Park from being replaced by a Las Vegas-type replica Ottoman-style shopping center.
Pictures of riot police attacking unarmed female and elderly protesters with tear gas and water cannons spread across social media, sparking outrage and spawning protest rallies in at least 67 cities in more than half of Turkey's 81 provinces.
But Arinc said his apology did not extend to other protesters who he said were out to wreak havoc.
"I apologize to those who gathered with sincere feelings in Gezi, but I don't owe any apology to others," he said in response to a reporter who asked at a news conference if the government owed an apology to those injured in the police crackdown.
If was not immediately clear if Arinc's limited apology had the approval of Prime Minister Recep Tayyip Erdogan, who previously dismissed all protesters as "looters," "bums" and an "extremist fringe."
Erdogan is on an official visit to Morocco until Thursday.
Arinc, who is acting prime minister while Erdogan is away, said the protest violence cost Turkey more than $37 million.
Two protesters were killed in the violence -- one run over by a taxi in Istanbul and the other shot in the head in the southern city of Antakya near the Syrian border, the Turkish Medical Association said.
The non-profit Turkish Human Rights Association said more than 2,800 protesters were injured nationwide, many seriously, and 791 were detained, although "around 500" were later released.
Arinc said Tuesday 244 police officers and 64 protesters were injured nationwide.
Separate from the Istanbul riot-control measures, police in the western city of Izmir arrested 25 people for sending "misinformation" over Twitter, the official Anadolu Agency reported.
Opposition leader Ali Engin of the Republican People's Party told the news agency the people were arrested for "calling on people to protest."
Erdogan said Sunday Twitter was a societal "menace" being used to spread "lies."
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