"I, without qualification, apologize for the pain and the hurt and the indignity and the damage that apartheid has done to Black, Brown, and Indians in South Africa," de Klerk said.
It was not immediately clear when the recording was made.
De Klerk, who was diagnosed with cancer earlier this year, is globally seen as a politician who negotiated a peaceful transfer of power from white-minority rule to a Black-majority democratic government led by Nelson Mandela.
He shared the Nobel Peace Prize with Mandela in 1993.
But in South Africa, many saw him as a controversial figure who had shown little remorse for the crimes committed during the apartheid regime.
"It is true that in my younger years, I defended separate development... I did so when I was a Member of Parliament, and I did so as I became a member of cabinet," said a frail looking de Klerk in a navy blue suit, in what he termed his last message to the country.
"Afterwards, on many occasions, I apologized for the pain and the indignity that apartheid has brought to persons of color in South Africa. Many believed me, but others didn't."
De Klerk sparked a widespread backlash last year when he told a national broadcaster that he did not believe apartheid was a crime against humanity.