Turkish Deputy Prime Minister Bulent Arinc expressed his regrets for "excessive violence" used on protesters in the last few days. His words come amid international condemnation of Turkey's handling of the situation.
Speaking on behalf of the Turkish government while Prime Minister Recip Tayyip Erdogan is on a trip to North Africa, Arinc regretted "the excessive violence that was used in the first instance against those who were behaving with respect for the environment."
The initial protests were started by activists opposed to the building of a shopping mall on an area of parkland.
Arinc told a news conference in the capital Ankara that it was "wrong and unfair. I apologize to those citizens."
"The government has learnt its lesson from what happened," he added. "We do not have the right and cannot afford to ignore people. Democracies cannot exist without opposition."
But he also said that the government didn't owe an apology to "those who have caused damage in the streets and tried to hinder people's freedom."
The comments stand in stark contrast to Erdogan's insistence on Monday that the protesters were "extremists" and "vandals."
The United States on Monday expressed concern about the reports of police using excessive force against demonstrators.
"We obviously hope that there will be a full investigation of those incidents and full restraint from the police force," US Secretary of State John Kerry said.
Earlier in the day, German Chancellor Angela Merkel called on the Turkish authorities to exercise restraint.
Last week, the peaceful local protest against plans to redevelop Gezi Park, near Taksim Square in Istanbul turned violent when riot police fired tear gas to clear hundreds of demonstrators. Two people have died since the protests erupted.
The Turkish Human Rights Association said some 3,300 people nationwide were detained during four days of protest, but that most had since been released. At least 1,300 people were injured, the group said, although it said the true figures were difficult to come by.
On Tuesday, hundreds of riot police backed by water cannons were stationed around Ankara's main square near the prime minister's office.
The main public sector union federation, the leftist KESK, which represents 240,000 members, launched a two-day strike on Tuesday, originally called over workers' rights, to protest at the police crackdown.
ng/rc (AP, dpa, Reuters)