His remarks came shortly before reports emerged of the first protester death since the street anger erupted on May 31.
The Turkish doctors' association TBB said a 20-year-old protester died when he was hit by a taxi in Istanbul. It was unclear when the incident occurred.
Hundreds of demonstrators and police have been reported injured, and the arrest total was nearing 2,000, many of them detained and then released.
On June 3, Erdogan maintained that antigovernment protests in Istanbul, Ankara, and other cities were organized by extremists.
"Regarding these incidents, as the prime minister and as a resident of Istanbul, I would like to say that should we put aside those who joined the protests with their naive emotional feelings following the calls from social media," he said. "[We will see that] there were extremist elements who organized these protests, and unfortunately people joined them."
Erdogan, who spoke in Istanbul before leaving on a North African tour which will include Tunisia -- the cradle of the Arab Spring revolts -- said those who call the current protests the "Turkish Spring" "do not know Turkey."
Meanwhile, Turkish President Abdullah Gul called for calm and said that peaceful demonstrations were a part of democracy. Gul added that the protesters' "messages delivered with good intentions have been received."
Also on June 3, Turkish police fired tear gas at demonstrators in the capital, Ankara, in the fourth day of protests against Erdogan's government.
In the western port city of Izmir, protesters threw fire bombs at Erdogan's ruling Justice and Development Party (AKP) offices overnight.
The demonstrations began on May 31 over what was felt to be excessive police force against protesters holding a sit-in to prevent the uprooting of trees in Istanbul's Taksim Square, but have since spiraled.
Protesters accuse Erdogan's Islamic-rooted AKP of gradually imposing Islamic rule on a staunchly secular Turkey.
One week before the protests began, Turkey banned alcohol advertising and placed restrictions on its sale.
Calls for restraint during the protests from Turkey's NATO allies Britain, France, and the United States were echoed by the European Union, whose foreign policy chief, Catherine Ashton, condemned the "disproportionate use
of force" by police.
U.S. Secretary of State John Kerry, speaking at a press conference in Washington on June 3, said the United States was troubled by reports of excessive force by police and "deeply concerned" by the number of people injured in the antigovernment protests.
Kerry also called for an investigation into the violence and urged all sides to "avoid any provocations or violence."
"We don't say these things to interfere in another country's choices or events, but we say these things to reaffirm what we believe are universal principles and values that are essential to the practice of democracy and to the improvement of the relationship between governments and people," Kerry said.