Former chief of state protocol Bruce Koloane says the final report into the Gupta Waterkloof landing in 2013 "smells fishy".

Koloane, who is now the South African ambassador to the Netherlands, was testifying at the judicial commission of inquiry into state capture on Monday.

The justice, crime prevention and security (JCPS) cluster investigated the landing after 200 guests of the Gupta family landed at the air force base in a commercial aircraft to attend the family's lavish wedding in Sun City.

"I want to go on record that the manner in which the final report was compiled by the JCPS smells fishy, and normally if it smells fishy, it is fish," Koloane told inquiry chairperson Deputy Chief Justice Raymond Zondo.

"The people that interviewed me, I would have expected that they are the people who are also associating with the document. Now, they are the people who have never sat with me at all, but they are the ones compiling the final report," he said.

Koloane has become known as the "fall guy" in the Waterkloof landing saga.

"I just want to go on record chair, to say I, as one of the people who was implicated, was never ever invited by the committee of four people ... so that they could sit with me and say that 'there are some contradictory information we have received which conflicts with the statement that you have given'. Never. So, I was never subjected to that.

"Second, one of the people in that committee it came out ... is that Mr Tom Moyane was part of that committee, but he never sat in meetings where I was interrogated by the committee…"

Koloane said he was never given an opportunity to interact with the information gathered by the committee.

He added the report was already in the public domain by the time he was called to give his account of the events.

Koloane claimed that during his first interaction with former director-general of justice and constitutional development Nonkululeko Sindane who chaired the JCPS – Sidane pronounced that he should not be allowed to use state funds to defend himself legally.

"I wasn't sure where that came from… I thought there was already a bias and when the report came in the way that it did, it definitely raised serious concerns on my side," he said.

Asked to identify factual inaccuracies in the report, Koloane said what Sindane referred to was that he (Koloane) told someone that the minister of transport approved the landing.

"Surely, surely, you will also appreciate that I won't be naïve to expect a minister of transport to supersede the minister of defence when Waterkloof is a base that falls under the authority of the minister of defence.

"Yes, the minister of transport spoke to me about the landing at OR Tambo, but never did I make reference to it landing at Waterkloof," Koloane said.   

Sidane, who had previously testified before the Zondo commission, said the JCPS cluster interviewed everyone involved in the incident, including the Gupta family, ministers, high ranking officials and the deputy director-general in the Presidency at the time.

He explained that former president Jacob Zuma was exonerated in this incident because he was never directly implicated by anyone in their investigations.

However, his name was used to get the permission needed. At the time, Koloane was accused of name-dropping Zuma in order to get consent, in particular.

Sindane said during the investigation, Koloane denied that Zuma had instructed him.

"There were references to 'Number 1' and we say this was abuse because … for at least Ambassador Koloane, we interviewed him and he denied being instructed [by Zuma]," Sindane said at the time.

During his testimony on Monday, Koloane said he had no authority to approve the landing.

He added the first time he had learned about the request was when he received a call from the Indian high commissioner.

Instead, he only asked for correct procedures to be followed in approving the flight clearance.

Koloane is expected to continue with his testimony on Tuesday.