The EFF has already raised objections to the much-anticipated state capture inquiry even though it could be months before it kicks off.
Party leader Julius Malema said at the party's Braamfontein headquarters on Thursday that the EFF was not happy with black senior counsels in the inquiry being supervised by a white superior.
He said the party also wanted the head of investigations in the commission, Terence Nombembe, to recuse himself.
Nombembe is the former Auditor-General and CEO of the South African Institute of Chartered Accountants (SAICA). Malema accused him of having accepted a donation from Gupta-linked company Trillian while at SAICA.
The red berets' commander in chief said the party would write to Deputy Chief Justice Raymond Zondo, who is chairing the commission, about a request for Nombembe to recuse himself.
Malema said if this doesn't happen the EFF would challenge the investigation leader's appointment in court.
On Wednesday Zondo said that Nombembe would lead investigations while Advocate Paul Joseph Pretorius SC a would lead the team of lawyers for the commission.
Three other top advocates who form part of the team are Khotso de Wee, Vincent Maleka and Thandi Norman.
R1.2m donation from Trillian
The commission, which was announced by former president Jacob Zuma a month before he resigned, is part of the remedial action ordered by former Public Protector Thuli Madonsela.
This followed her investigation into claims that members of the Gupta family had undue influence over Zuma and his executive as well as operations at state owned enterprises. The project is said to have resulted in the theft of billions of taxpayers' money.
"Deputy Chief Justice Zondo is starting on a wrong footing (sic), I am telling you now. I am warning you South Africa, here we are up to something," said Malema.
He said though he believed the intention might have been good, things might not end well, as the composition of the commission seemed suspicious.
In response, spokesperson for the Office of the Chief Justice, Nathi Mncube, said they had just noted the concerns by Malema, as well as his intention to pen a missive for Zondo's attention.
He said the commission was of the view that it was advisable to wait for the missive to reach Zondo before commenting.
Malema said Nombembe, in his position as CEO at SAICA received a R1.2m donation from Trillian Capital, which is implicated in the Gupta scandal, and that when the EFF in Parliament tried to get confirmation from him, he instead wanted to discuss the matter via telephone.
"By the time SAICA received the donation it was common cause and public knowledge that Trillian Capital was used as a corruption vehicle by the Guptas' criminal syndicate and had received more than R500m from Eskom," said Malema.
Malema said the EFF believed Nombembe's attempt to discuss the matter telephonically instead of giving a written reply could have been because he wanted to bribe their leadership collective in the National Assembly.
"Nombembe must answer to the commission. How is he going to answer when he is the investigator himself?" questioned the firebrand leader.
Whites supervising blacks
Malema said he did not understand why a white senior counsel was placed in charge of three capable black advocates.
"At the end of everything else when all this corruption is exposed and people are being prosecuted it must be [said] that it took white fellows to intervene in the state capture otherwise there would not have been a stoppage of corruption in South Africa," said Malema.
The EFF leader questioned the constant need for black people to be supervised by whites, adding "we are not happy here".
Although he applauded the inclusion of female senior counsels in the teams, he took issue with Advocate Thandi Norman.
"We question the appointment of Thandi Norman SC who is a direct appointee and representative of Jacob Zuma in the Judicial Service Commission (JSC). While we may accept her personal integrity it is irrelevant on a question of conflict of interest," said Malema.
"How can someone who was handpicked by Zuma to represent him in the JSC act neutrally in a position in which the same Zuma stands as the principal person accused of masterminding state capture?" asked Malema.
After warning that the commission could be a waste of taxpayers' money, Malema said the party would keep close watch over it to see how it unfolds.
Nombembe could not be reached immediately for reaction to Malema's comments.