This was after The Times reported that Skinner and Sibiya wrote a 15-page letter of resignation this week to Judge Willie Seriti, who chairs the commission.
In the letter, they claimed they were being treated disrespectfully by the commission’s head of legal research, Advocate Fanyana Mdumbe.
President Jacob Zuma announced the establishment of the commission, chaired by Seriti, in October 2011.
Its aim is to investigate alleged corruption in the country’s multi-billion rand arms procurement deal.
Since the announcement, the commission has been dogged by claims that its integrity might be compromised.
Judge Willem van der Merwe resigned in 2011 for personal reasons, immediately after being appointed by Zuma as a commissioner.
He was replaced by Free State Judge President Hendrick Musi.
In January last year, senior commission investigator Norman Moabi quit.
Moabi, a lawyer and former acting judge from Pretoria, alleged in a letter, leaked to Beeld newspaper, that the commission was not being transparent and concealing an alternative or “second agenda”.
According to Moabi, Seriti ruled the commission with an iron fist and facts were manipulated or withheld from commissioners. Contributions from commissioners who did not pursue the “second agenda” were frequently ignored.
Law researcher Kate Painting resigned last March, followed by commissioner Judge Francis Legodi last August.
In April this year, chief evidence leader Tayob Aboobaker resigned.