Ismail Akoo`s voice shook when he said he had "no idea" how to deal with information that Darul Uloom Newcastle featured in a 2010 document titled Operational target analysis.
The document states that in KwaZulu-Natal, a person, whose name has been blocked out, was running a special training camp for Muslim students.
It goes on to state that the person stemmed from the school but was born in Cape Town.
"He is known to have links with the Taliban of Afghanistan and is a known Mujahedin fighter. He is known for extremist views and is not scared to make militant statements."
Akoo on Tuesday said it was the first time that he heard of "such a thing".
The document, which was obtained by UAE based TV station Al Jazeera, lists Iran`s interests in South Africa, including setting up front businesses, and trying to secure military technology.
The dossier also stated that they were funding training for a Jihad against the United States.
It added unconfirmed reports of a unnamed farm near Port Elizabeth, that provides training.
"I don’t even know what to say. This is a surprise to me. How does one deal with this?" said Akoo
"I have been at this school for 25 years and had even been a student here. This is a small community. If a former pupil was involved in something like this, I would have heard about it," he said.
Akoo said the pupils were taught religion which did not believe in terrorism.
"This is why I am finding it so hard to believe. Those who have been taught here, know that terrorism does not feature in Islam," he said.
Another Islamic institution that was identified in the report was the Darul Uloom Zakariyya in Zakariyya Park, south of Johannesburg.
The report said that school had regular training sessions for South African students and foreigners in order to keep them ready for a possible Jihad against the US aggression in the Middle East.
The principal of the Darul Uloom Zakariyya, Shabbier Ahmed Saloojee, said it was wholly untrue.
“This allegation was printed under the South African Operational Target Analysis of Iran, whereas our institution is a strictly Sunni institution, who are diametrically opposed to Shiasim and we have no ties to Iran or any country”, he said in statement.
He went further to say that students at the institution were directed to distance themselves from all politics and anything that brings the institute or the country into disrepute.
Saloojee demanded an apology from Al Jazeera.
The report also accused the Ahl-ul-Bait foundation, based in Cape Town, of disseminating Iran propaganda and “promoting the concept of the Iranian revolution”.
The foundation responded that they are a purely religious organisation.
“These are just allegations. There is no evidence that what is being said in the report is true. We are not political, not on a national or international level,” he said.
“Our activities are purely spiritual, we also have many interfaith activities. That is all I want to say,” said Sheik Syed Haider.
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