Erdogan told a sea of flag-waving supporters that two weeks of protests had been manipulated by "terrorists" and dismissed suggestions that he was behaving like a dictator, a constant refrain from those who have taken to the streets.
Riot police fired teargas into side streets around the central Taksim Square as he spoke, trying to prevent protesters from regrouping after hundreds were evicted from the adjoining Gezi Park, the centre of the protests, late on Saturday.
"They say 'you are too tough', they say 'dictator'. What kind of a dictator is this who met the Gezi Park occupiers and honest environmentalists. Is there such dictator?," Erdogan said to roars of approval from the crowd.
"The attitude across Turkey with the pretext of Taksim's Gezi Park is not sincere. It is nothing more than the minority's attempt to dominate the majority ... We could not have allowed this and we will not allow it," he said.
Bulldozers removed barricades and municipal workers swept the streets around Taksim, sealed off by police on Sunday after thousands took to the streets overnight following the raid by riot police firing teargas and water cannon.
The umbrella protest group behind the Gezi Park campaign, Taksim Solidarity, called for demonstrators to gather peacefully again in the square, but Istanbul Governor Huseyin Avni Mutlu made clear they would not be allowed to do so.
"Any call for (people to gather in) Taksim will not contribute to peace and security," he told reporters, as riot police fired teargas in several locations to disperse groups of demonstrators trying to reach the square.
"After the current environment becomes stable, they can continue exercising their democratic rights. Under current circumstances we will not allow any gathering."
Erdogan, who also addressed supporters of his ruling AK Party in Ankara on Saturday, said the rallies were to kick off campaigning for local elections next year and not related to the protests, but they are widely seen as a deliberate show of strength.
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The blunt-talking prime minister has long been Turkey's most popular politician, overseeing a decade of unprecedented prosperity, and his AK Party has won an increasing share of the vote in three successive election victories, but his critics complain of increasing authoritarianism.
While the protests pose no immediate threat to his government, they have tarnished Turkey's image as a haven of stability in a turbulent Middle East.
Two union federations said on Sunday they would stage a one-day nationwide strike on Monday in protest at the forced eviction of the Gezi Park protesters.
The protesters, who oppose government plans to build a replica Ottoman-era barracks in the leafy park adjoining Taksim Square, had defied repeated calls to leave but had started to reduce their presence in the park after meetings with Erdogan and the local authorities.
A similar police crackdown on peaceful campaigners in Gezi Park two weeks ago provoked an unprecedented wave of protest against Erdogan, drawing in secularists, nationalists, professionals, trade unionists and students.
The unrest, in which police fired teargas and water cannon at stone-throwing protesters night after night in cities including Istanbul and Ankara, left four people dead and about 5,000 injured, according to the Turkish Medical Association.