A tearful whistleblower into the alleged looting of the Secret Service Account (SSA) within Crime Intelligence (CI) has apologised for his role in the alleged criminality and corruption that took place in the police unit.

"During my time at CI, I made decisions that I truly regret and I am sorry for my actions," an emotional Colonel Dhanajaya Naidoo told the Commission of Inquiry into State capture on Wednesday.

He further addressed the notion that he turned into a section 204 witness in a bid to escape prosecution for his role in the alleged looting.

"It was my wife who convinced me to come clean. On the 19th of October 2011 I came clean at my own accord. There was a version put forward that I did this for a deal to escape prosecution. This is not true. On the 19th I went there on my own accord with no lawyers and with the prospects of being arrested myself.

"The suggestion that I did this to get a deal for myself is totally untrue. The decision on whether I will be treated as a section 204 witness will unfold in the courts. I am ready to face the consequences of my own actions," he added.

Naidoo previously admitted that he took advances for personal gain to the tune of R100 000 and traveled abroad, as well as locally on the SSA account.

Naidoo was placed in the witness protection programme on October 25, 2011. 

"I can't go into detail about witness protection, but chair it has been extremely difficult. Next month will be eight years in witness protection. The first few years my children spent their prime years in protection.

"We live on a month to month basis. We cannot be planning for anything beyond a month. I am hoping that me testifying will give some urgency to the processes that are still outstanding," he said.

A senior Hawks investigator who probed the alleged looting of the SSA previously told the Commission that the classification of documents was frustrating.

Colonel Kobus Roelofse told the commission that the refusal to declassify documents frustrated his investigations over the past seven years, News24 reported.

Chair of the Commission, Deputy Chief Justice Raymond Zondo said that although he could not begin to imagine a life in witness protection, he thanked the witness for his evidence.

"I have no idea what it must be like to be in witness protection.  I have no idea what it must be like to have your whole family in the programme for one year, I have no idea what it is like to have your whole family in the witness protection programme for seven or eight years. Your freedom of movement is very limited and you live a life that is very unlike the life you lived before going into the programme.

"I must thank you Col.  Naidoo for coming forward to give evidence to the commission. Persons who are implicated by you in their evidence will be given opportunities to apply for leave to cross-examine you and give evidence themselves. I do not know what conclusions I will reach later when I look at you evidence as well the evidence of those implicated," Zondo said.

Naidoo testified over 4-days in-camera at a secret location.