Charles used a speech, delivered during a banquet in Kenya held in his honour, to speak of the "greatest sorrow" and "deepest regret" for the "wrongdoings" of the past, a period when Britain's colonial administration violently put down Kenya's battle for self-rule.
Kenya's President William Ruto praised the King's "exemplary courage" in shedding light on "uncomfortable truths" but described the colonial reaction to African struggles as "monstrous in its cruelty" and said "much remains to be done in order to achieve full reparations".
Kenya's uprising, commonly known as the Mau Mau rebellion, was an armed movement that began in the early 1950s, fuelled by the resentment some members of the Kikuyu tribe felt towards their British rulers, European settlers who farmed land in Kenya and a lack of political representation.
White farmers were targeted in violent attacks and Kikuyu said to have collaborated with the authorities during the unrest known as the Emergency.
The Kenya Human Rights Commission has claimed 90,000 Kenyans were executed, tortured or maimed during the British administration's counter-insurgency.
Speaking after Mr Ruto, Charles told the 350 banquet guests gathered at the president's official residence in the capital Nairobi: "It is the intimacy of our shared history that has brought our people together.
"However, we must also acknowledge the most painful times of our long and complex relationship.
"The wrongdoings of the past are a cause of the greatest sorrow and the deepest regret.
"There were as they waged, as you said at the United Nations, a painful struggle for independence and sovereignty, and for that, there can be no excuse.
"In coming back to Kenya, it matters greatly to me that I should deepen my own understanding of these wrongs, and that I meet some of those whose lives and communities were so grievously affected."
The King and Queen spent the first full day of their five-day state visit acknowledging the sacrifices of Kenyans, with Charles laying a wreath at the Tomb of the Unknown Warrior in Nairobi's Uhuru Gardens National Monument and Museum.
The tomb recognises Kenya's fallen heroes, military and civilian, and Charles' floral tribute had a handwritten note which read: "In grateful remembrance - Charles R".
In 2013, the British government made a statement of regret over the "torture and other forms of ill treatment" perpetrated by the colonial administration during Kenya's Emergency period of 1952-1960, and paid out £19.9 million ($A38 million) to about 5200 Kenyans for human rights abuses.
The development came after a legal battle between a number of elderly victims and the British government.
The president said in his address: "If colonialism was brutal and atrocious to African people, colonial reaction to African struggles for sovereignty and self-rule was monstrous in its cruelty.
"It culminated in the Emergency, which intensified the worst excesses of colonial impunity and the indiscriminate victimisation of Africans.
"While there have been efforts to atone for the death, injury and suffering inflicted on Kenyan Africans by the colonial government, much remains to be done in order to achieve full reparations."
