Thanassis Stavrakis/AP Photo

Turkish anti-government protesters camped out in Istanbul's Hüseyin were awakened this morning by riot police who had largely left them alone for the past week and a half as they carried out their demonstrations.

The police said they came in to clear the square of the many banners that have been hung, firing water cannon and tear gas at the demonstrators who responded with rocks and Molotov cocktails.

Istanbul's governor said the police's actions were not aimed at harming the protesters but rather in order to remove the many banners he described as "an advertisement billboard of legal and illegal organizations."

The banners were "upsetting the public, as well as harmful to Turkey's image abroad," Hüseyin Avni Mutlu said at a press conference, according to Turkey's Hurriyet newspaper, adding that those clashing with the police were "marginal groups," not mainstream demonstrators.

At least one police vehicle was set on fire.

Turkey has seen nationwide protests for almost two weeks against the government of Prime Minister Recep Tayyip Erodgan, whom the protesters accuse of growing increasingly authoritarian after a decade in office. Three people have died and thousands have been injured.

The recent round of violent clashes - the biggest protests Turkey has seen in decades - were sparked by a much smaller demonstration in Taksim's Gezi Park two weeks ago. Demonstrators had turned out to protest the building of Ottoman barracks in the park that would also include as a shopping mall. When the police responded heavy-handedly, spraying demonstrators with pepper spray, it triggered the much larger protests.

Istanbul's police retreated from the square soon after the protests broke out, but skirmishes continued on side streets and elsewhere in the city as protests sprang up around the country. Erdogan responded defiantly, calling the protesters "looters" and "extremists" and threatening to turn out one million of his own supporters in response.

"Violent actions that took place in many cities of Turkey have camouflaged themselves behind the Gezi Park protests," Erdogan said in a speech to parliament on Tuesday. "I request all activists to see the big picture, understand the plot, and withdraw from the streets."

Erdogan pointed to his party's repeated successes at the ballot box as evidence of support from the majority of Turks. The protesters had said Erodgan is behaving increasingly like a dictator and is imposing a stricter brand of Islam on the famously secular country. Turkey recently passed a law restricting the hours of sale of alcohol and Erdogan has talked about restricting abortion and saying that families should have three children.

"Freedom and intervention in lifestyles are excuses used by the protesters," Erdogan said, according to Hurriyet. "The hotels in Taksim are now 80 percent empty, the shopkeepers in Taksim are suffering - except the beer sellers. This is intervening with others' freedom."

Erdogan is set to meet with leaders of the protest movement on Wednesday, but the clashes have raised doubts about whether the meeting will happen.