"We have noticed that there is a perception that the commission cannot find Mr Fana Hlongwane, one of the people against whom allegations of wrongdoing in the arms acquisition process have been levelled," spokesperson William Baloyi said in a statement.
"We wish to make it clear that the commission has been in contact with him through his attorneys and it is not true that he cannot be traced."
He said Hlongwane was part of the list of witnesses for the second phase of the commission.
The Mail & Guardian reported on Friday that Hlongwane, who was allegedly paid R65-million in arms deal bribes, apparently could not be found and had been removed from the list of witnesses released this week.
At the end of 2011, President Jacob Zuma appointed a commission of inquiry under Judge Willie Seriti to investigate allegations of corruption surrounding the multibillion-rand arms deal.
Earlier this year, Seriti claimed Hlongwane could not be traced and, therefore, had not been issued with a subpoena.
The M&G reported Hlongwane was evidently tipped off that his office and home would be raided by the Scorpions in 2008. Because of the tip-off, four boxes of evidence were allegedly removed from his office just before the raid.
The raids were part of the Scorpions's investigation into arms deal corruption.
The commission's public hearings are scheduled to start on August 5.
On Monday, Baloyi announced that former president Thabo Mbeki and Minister in the Presidency Trevor Manuel were set to testify in the second half of January.
Baloyi said the first phase of the commission would "deal with the rationale for the strategic defence procurement package", and whether the arms and equipment acquired were under-utilised or not utilised at all.
The first witnesses would be navy and air force officials. Armscor witnesses would be named later.
Former intelligence minister Ronnie Kasrils and Congress of the People leader Mosiuoa Lekota would be called as witnesses between September 30 and October 4, followed by trade and industry department officials until November 11.
Former public enterprises minister Alec Erwin was expected to testify for three days in November, followed by national treasury officials until the end of that month.
The commission will be held in the council chambers of the Sammy Marks Conference Centre in Pretoria. – Sapa