He denied that he ever accused national director of public prosecutions Bulelani Ngcuka of abusing his powers due to past obligations to the apartheid regime.
"Those were not my words, those are the terms of reference's words," Maharaj testified in cross-examination before judge Joos Hefer.
Maharaj conceded that he suspected Ngcuka of having an ulterior motive in investigating and pursuing him and other leading African National Congress members, as head of the prosecuting authority.
However, that motive could have many bases, Maharaj held.
It was not necessarily linked to Ngcuka's alleged selling out of former comrades to the apartheid government.
Advocate Norman Arendse, representing Justice Minister Penuell Maduna, accused Maharaj of "beating around the bush".
Arendse said the terms of reference, changed last week to specifically name Maharaj and Mo Shaik and Ngcuka's main accusers, remained in effect the same.
Since the establishment of the commission, President Thabo Mbeki has changed its terms of reference thrice.
Maharaj said yesterday he would prefer the commission to stick to the terms as after the first change.
These did not name him and Shaik as Ngcuka's accusers, with their allegations described as triggering the inquiry.
Maharaj further admitted on Tuesday that he accepted former Eastern Cape human rights lawyer Vanessa Brereton's confession that she was apartheid agent RS452.
This was despite his and Shaik's earlier conclusion that Ngcuka was most probably the agent operating under that code name.
However, Maharaj said yesterday, Brereton's confession still did not resolve the question whether Ngcuka was an apartheid spy.
He suggested that information provided by Ngcuka to the apartheid government could have been contained in reports written under RS452's name.
This was in line with the former security forces' common practice of "false flagging" to protect its informants, Maharaj said.
The hearing continues. – Sapa.