Phosa told the Cape Town Press Club he rushed to get clarification from Zuma after he appeared to question the role of the country's highest court in an interview published in Independent Newspapers' titles last week.
"The morning after, I had a discussion with him because I wanted to be clear the context in which it was said."
But he said he was reassured that "there is no ANC policy that we must change the Constitutional Court".
He said Zuma took issue with remarks attributed to Deputy Chief Justice Dikgang Moseneke just after the African National Congress's watershed conference in Polokwane in 2007 where Zuma was voted in as party leader.
Moseneke reportedly told guests at a birthday party: "I want to use my energy to help create an equal society. It's not what the ANC wants or what the delegates want: it is about what is good for our people."
Phosa said Zuma felt it was not healthy for judges to "reduce themselves" to expressing personal opinions about political parties.
"They should not show their preferences, they should not lower their guard."
In the interview published three days after the National Prosecuting Authority withdrew fraud and corruption charges against Zuma, the presidential front-runner said a democracy could not have "people who are almost like god".
He said Constitutional Court judges were fallible and called for the Judicial Service Commission to review the status of the court.
"As the president of the country... I think it's important to engage them, to raise these kinds of issues in their organisation," he said.
Phosa called on South Africans to accept that the fact that the charges against Zuma were dropped, saying those who insisted he was guilty were violating his right to be presumed innocent.

