Motsoeneng said it was "insulting" to President Jacob Zuma, he admitted to the Mail & Guardian.
The controversial executive, known as Zuma's SABC enforcer and the person who has been wielding the censor's axe in the run-up to Mangaung, said the broadcaster's political editor, Abbey Makoe, had raised the alarm about the interview that was supposed to go out on the programme Interface and he had agreed not to run it.
After finally viewing the Interface interview on Thursday morning, Motsoeneng told the M&G there was "no way we could carry it". The show was scheduled to be aired on Sunday.
"The cartoons shown are all about President Jacob Zuma and Zapiro is justifying his own cartoons," he said. "We are very sensitive about all people's rights and dignity and so we could not carry that interview. Zapiro must do what he does best, but we disagree and we can't endorse his cartoons on our platform."
Motsoeneng said he was not practicing censorship at the SABC.
'Ultimate nutcase deployment'
"It is about balancing the story. If you talk about Hlaudi and I am not there, we can't run it. We also can't use it if you insult other people."
Asked why the SABC could not interview Zuma and still use the Zapiro interview, Motsoeneng said: "The first issue with the interview was that it was not balanced. The second was that we could not put those cartoons on air. It was not as if the only thing is to try to balance the story – I couldn't condone those cartoons."
Shapiro said this was the third time an SABC interview with him had been cancelled recently and he was concerned that he was being "blacklisted". The other two occasions were SABC radio interviews on Metro FM and 5FM set up by Shapiro's publishers last month to promote his latest annual of cartoons, But will it stand up in court?. The interviews were cancelled a few days before their scheduled airing. The producers' excuse was that they had been told not to carry anything political.
"If it weren't so serious it would be a joke," said Shapiro. "My sense is that it is not always direct orders from Luthuli House that gets people in executive positions to make these decisions."
Shapiro insisted as a condition for the Interface interview that some of his cartoons be shown. The main cartoon was one featured in the M&G depicting Zuma's famous showerhead emitting a jet of water to extinguish the flame of Lady Justice.
Shapiro described Motsoeneng as the "ultimate nutcase deployment".
"Motsoeneng does seem to be an extreme version of weird deployments. He doesn't know how to do his job properly and he is trying to curry favour."
The SABC's road to the ANC national conference in Mangaung has been filled with more intrigue than any of its soap operas.
Following its controversial decision last week to pull Sakina Kamwendo's Metro FM talk show on Mangaung, the SABC has now tasked its head of news and current affairs, Jimi Matthews, with control of all radio talk shows that deal with politics and governance.
Motsoeneng said this had been done to avoid a repeat of the debacle in which the talk show featuring three political journalists was cancelled at the last minute because no representative of the ANC had been invited. The show was resurrected this week with secretary general Gwede Mantashe on hand to give the ruling party's views.
Motsoeneng said management was not taking seriously an unsigned letter sent to Matthews and SABC chief executive Lulama Mokhobo by journalists this week. "Since I arrived here at the SABC, it has been a very stable place," he said.
He chuckled when asked how he would find an ANC representative for all the talk shows and current affairs programmes on the many radio stations and television channels of the SABC. "If we invite an ANC representative and they don't pitch up, then the show must go on."
Meanwhile, a number of charismatic church leaders assembled at the SABC headquarters in Johannesburg on Thursday to pray for the broadcaster's leadership.
Some of the churchmen spoke in tongues, including one in a strong American accent, and laid their hands on Motsoeneng and Mokhobo.
One of them, Bishop Pule Magethi of the Setshabelong Bible Church, said: "If you have leadership that stands for unbiased programming, which will not paint anyone in a bad light, then that executive needs our support. The SABC has the power to make or break our nation."
Since the SABC leaders took this decision, lots of "nonsense" had appeared in the media, said Magethi. – Additional reporting by Madelene Cronjé