This comes after comments Zuma made at a memorial service for struggle hero Chris Hani were interpreted as a side-swipe at Manuel, who last week said apartheid could not be blamed for current failings in delivery.
On Wednesday, President Jacob Zuma said it was impossible to see complete change in just 20 years. The damage done by apartheid would be with the country for some time, he said.
"To suggest we cannot blame apartheid for what is happening in our country now, I think is a mistake to say the least," Zuma said at the 20th anniversary of South African Communist Party (SACP) leader Chris Hani's assassination.
"We don't need to indicate what it is apartheid did. The fact that the country is two in one, you go to any city there is a beautiful part and squatters on the other side. This is not the making of democracy and we can't stop blaming those who caused it," said Zuma.
But in a statement released on Thursday, the presidency sought to clarify these statements.
"Stating that the apartheid legacy and impact still exist and will linger on for a long time does not mean that the president is saying that public servants should use it to excuse laziness and incompetence."
"The impact of 300 years of apartheid and colonialism will be felt for many years to come and since 1994 government has been working to reverse it. However, stating this fact, does not excuse laziness and inefficiency," it further stated.
Blaming apartheid
The debate was sparked by a speech made by Manuel at a conference of the Senior Management Service.
Speaking at the conference, Manuel said: "We cannot continue to blame apartheid for our failings as a state. We cannot plead ignorance or inexperience. For almost two decades, the public has been patient in the face of mediocre services. The time for change, for a ruthless focus on implementation has come."
Several public figures have joined the debate in recent days.
ANC secretary general Gwede Mantashe appeared to agree with Zuma's perspective, saying that "apartheid will not vanish into thin air" and that South Africans should "appreciate the impact of this evil system on the society".
SACP deputy general secretary Jeremy Cronin defended Manuel's comments, saying his remarks were intended to encourage civil servants to be proactive in delivering services.
"What [the] comrade was actually saying … which weren't on the banner headlines [was] we need a strong and effective government [or] we will not be able to reverse the effects of apartheid on the opportunities available to all South Africans".