Testifying before the Truth and Reconciliation Commission at a special hearing in Cape Town, de Klerk said the NP was making the renewed apology in the full knowledge of the tremendous harm apartheid had caused millions of South Africans.
"I apologise in my capacity as leader of the NP to the millions who suffered wrenching disruption of forced removals; who suffered the shame of being arrested for pass law offences; who over the decades suffered the indignities and humiliation of racial discrimination."
He told a panel chaired by TRC chairman Archbishop Desmond Tutu a perception had developed that the NP was not accepting overall responsibility for its part in the conflict of the past and that it was leaving the security forces in the lurch.
"Let me state clearly that the National Party and I accept full responsibility for all our policies, decisions and actions. We stand by our security forces who implemented such policies and decisions and all reasonable intepretations thereof."
The NP accepted that its security legislation and successive states of emergency had created circumstances conducive to many of the abuses of human rights which occurred.
"We acknowledge that our implementation of unconventional projects likewise created such an atmosphere."
However, many things had happened which the NP had not authorised or been aware of.
"The recent information of atrocities I find as shocking and abhorrent as anybody else."
As State President, he had gone out of his way to get to the bottom of the truth and to find and prosecute perpetrators of "dastardly" deeds.
He had never condoned gross human rights violations and rejected suggestions that the violations had ever been the policy of the NP or the then government.
The new South Africa was as much the creation of the NP as any other party, he said.
"We refuse to allow any party or any organ to deprive us of our rightful place in our new society. We do not regard ourselves as being morally superior - or inferior - (to) any other party."
De Klerk is to be closely questioned on his party's second submission to the TRC on Wednesday by commission national investigations director Glenn Goosen.
In welcoming de Klerk to the hearing, Tutu gave him notice that the TRC intended putting hard and painful questions.
However, he also paid tribute to de Klerk's role when South Africa had been facing comprehensive and utter disaster.
"You played a crucial role in this critical hour of our history."
De Klerk was accompanied to the hearing by NP MPs David Malatsi, Sheila Camerer and Marthinus van Schalkwyk, and the former director-general of his presidential office, Dave Stewart.