Reverend Barney Pityana's comments about the country's leaders were disappointing and unfortunate, the Presidency said on Tuesday.
"Some of the comments attributed to Dr Pityana stoop way below dignified public discourse and intellectual engagement," presidential spokesperson Mac Maharaj said in a statement.
"They are not worth repeating save to caution once again that disagreements are welcome in a democratic society, but should take place within the bounds of common human decency, without promoting a culture of hurling insults."
According to the Dispatch Online, Pityana told South Africans to take responsibility for the country's failures because they elected leaders without vision and basic competence.
"We must blame nobody but ourselves for the tragedy of our education system, a collapsing health care system, a bloated but inefficient civil service, pervasive crime, and corruption that has become endemic," Pityana was quoted as saying.
"That is because we have elected a government without any intelligence collectively to understand what must be done. We have a government trapped in ideological blinkers, that believes and behaves like it is unaccountable."
He was speaking in Grahamstown on Monday at Kingswood College's annual memorial lecture to celebrate the life of anti-apartheid activist Neil Aggett.
Pityana said the government was not dealing with matters such as unemployment.
"Instead it is reported public resources are being manipulated to enrich the few and to build a monument to Jacob Zuma's presidency by establishing a new town on Zuma's doorstep in Nkandla. And through it all this nation is fast asleep," he was quoted as saying.
Maharaj said some of Pityana's comments were incorrect and misleading.
Nkandla was not the only village receiving attention from government, he said.
The Nkandla smart growth centre was part of the KwaZulu-Natal government's programme to revive small rural towns.
Other towns that were part of the programme included Ndumo, Manguzi, Msinga, Mbumbulu, Nkandla, Charlestown, Jozini, Ngwavuma, Dududu, Weenen and Colenso.
"There are various other rural development projects by other government departments, nationally and provincially (sic), in various rural towns and villages," said Maharaj.
"We wish to emphasise that no government funds have been committed specifically to the Nkandla Mlalazi Smart Growth initiative."
In his speech, Pityana reportedly said the ANC and its allies treated with suspicion and hostility any ideas that did not reinforce their own "stereotypical reality" and sought to silence the likes of The Spear artist Brett Murray, cartoonist Jonathan Shapiro (Zapiro) and expelled ANC Youth League president Julius Malema.
Maharaj said: "We expect Dr Pityana to know that allegations do not mean people are guilty, and even more so in the case of the rape accusations, as the president was acquitted in a court of law."