Speaking at the launch of the Mpumalanga Times newspaper, he challenged South Africans, and particularly the media, to guard against a tendency to criminalise the just struggle against apartheid.
"There is an unbecoming tendency developing which seeks to equate the struggle against apartheid with those who enforced it, despite the fact that apartheid was declared a crime against humanity by the United Nations," he said
"I view this as an unbecoming tendency because you cannot equate the attack on a military base in Pretoria by liberation forces with the KwaMakutha killings."
On ANC members applying for amnesty to the Truth and Reconciliation Commission, he said: "I hope not to be misunderstood, as this has previously happened.".
If ANC members had acted outside the organisation's policies and committed human rights violations they definitely had to apply for amnesty.
Similarly if the TRC's investigations found any human rights violations then "we should apply for amnesty", Phosa said.
However, the ANC would not apply for amnesty for legitimate acts against apartheid.
There was no way that Franklin Roosevelt, Joseph Stalin and Winston Churchill - who headed the allied effort against Nazi Germany - could have been prosecuted for war crimes at the Nuremburg tribunal.
"In the same vein, there is no way we would have asked Moses to apply for amnesty for liberating the children of Israel from bondage. Why then, should the freedom fighters of South Africa be treated differently?, Phosa said.
He hoped the matter would now be laid to rest and that it would not be suggested the ANC wanted to politically co-opt the TRC.
Phosa also suggested an anti-racism monument with an eternal flame should be erected to remind South Africans never again to treat any human being as they were treated in the past.