At a news conference before a trip to Morocco, Recep Tayyip Erdogan said the protests were organised by extremists and accused the opposition of provoking “his citizens”.
For a fourth night, there have been confrontations between police and protesters with tear gas being used.
A protester has died after being hit by a taxi on Sunday, doctors say – the first fatality since the unrest began.
The demonstrator, 20-year-old Mehmet Ayvalitas, was hit when the car ignored warnings to stop and ploughed into a crowd of protestors in the Mayis district of Istanbul, said the Turkish Doctors’ Union.
On Monday evening, thousands of demonstrators again gathered in Taksim Square, the focus of the recent protests.
A helicopter, its searchlight shining onto the crowd, hovered overhead and tear gas wafted into the square.
Many protesters shouted “Tayyip, resign!” while waving red flags and banners and blowing whistles, according to the AFP news agency.
Police also fired tear gas again to disperse protesters near Recep Tayyip Erdogan’s office in the Besiktas district of Istanbul.
Earlier on Monday, protesters clashed with police in the capital, Ankara. Tear gas and water cannon were fired at hundreds of demonstrators in the city as around 1,000 protesters converged on central Kizilay Square.
In another development, a public sector trade union confederation, Kesk, says it will begin a two-day strike starting on Tuesday in support.
The left-wing confederation accused the government of being anti-democratic and carrying out “state terror”.
Shares in Turkey fell sharply as fears that the protests could continue took hold, with the main share index falling by 10.47%. The cost of insuring Turkish debt rose to a two-month high.
In a sign of continuing concern in Washington, Secretary of State John Kerry spoke of “excessive use of force” by the police.
“We obviously hope that there will be a full investigation of those incidents and full restraint from the police force,” he said.
Recep Tayyip Erdogan said during a televised news conference: “There are those attending these events organized by extremists. This is not about Gezi Park anymore. These are organized events with affiliations both within Turkey and abroad.
“The main opposition party CHP has provoked my innocent citizens. Those who make news [and] call these events the Turkish Spring do not know Turkey.”
Meanwhile, Turkish President Abdullah Gul urged calm and defended protesters’ rights to hold peaceful demonstrations.
“If there are different opinions, different situations, different points of view and dissent, there is nothing more natural that being able to voice those differences,” he was quoted as saying by the Anatolia news agency.
“The messages delivered with good intentions have been received.”
Protesters say the Turkish government is becoming increasingly authoritarian.
They fear Recep Tayyip Erdogan’s Justice and Development Party (AKP) is trying to impose conservative Islamic values on the officially secular country and infringe on their personal freedoms, correspondents say.
Officials say more than 1,700 people have been arrested in demonstrations in 67 towns and cities, though many have since been released.
On Sunday night, protesters in Besiktas tore up paving stones to build barricades, and Istanbul police responded with tear gas and water cannon.
Mosques, shops and a university in Besiktas were turned into makeshift hospitals for those injured in the demonstration.
Several thousand people took part in the protest outside the recently decommissioned Besiktas football stadium.
Unrest was also reported on Sunday in the western coastal city of Izmir, Adana in the south and Gaziantep in the south-east.
Last week, the government passed legislation curbing the sale and advertising of alcoholic drinks.
The protests began on a small scale last week in opposition to plans to redevelop Gezi Park in Istanbul but have since taken on wider political demands.
The demonstrators say the park is one of the few green spaces in Istanbul, and object to the loss of public space for commercial purposes.
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