Thousands of Turkish soldiers and Kurdish militants have been killed since fighting between the separatist Kurdistan Workers' Party, known by its Kurdish initials PKK, and the military began in the 1980s.
The PKK is considered a terrorist organization by the Turkish and U.S. governments.
Erdogan told lawmakers from the ruling Justice and Development Party that errors were made during the conflict.
"Severe destruction was carried out in the (Kurdish) region in the name of fighting terrorism," he was quoted by Turkish newspaper Today's Zaman as saying. "Inhumane treatment of mothers and fathers right in front of their children left indelible traumas in the psyche of many children."
His statement comes as Ankara tries to find solutions to Kurdish minority issues by reaching out to jailed PKK leader Abdullah Ocalan.
In early January, three elite figures from the PKK were killed at a Kurdish center in Paris. The Turkish newspaper reports that the pro-Kurdish Peace and Democracy Party had suggested Ankara was behind the attacks.
"When the truth is brought to light, those who accused the government and the state will be embarrassed," Erdogan said.
Some leaders in Ankara suggested the Paris attack may have been an inside job carried out by ultraconservative PKK supporters.