The Seriti commission probing the arms deal will respond later this week to allegations contained in a resignation letter by a senior investigator.

"The commission will send a comprehensive response on or before Wednesday January 23," spokesperson William Baloyi said on Monday.

Norman Moabi, a lawyer and former acting judge from Pretoria, alleged in the letter, which was leaked to Beeld newspaper, that the commission was not being transparent and was concealing an alternative or "second agenda".

Moabi wrote in the letter, addressed to Judge Willie Seriti, that he was resigning because of interference and because he had lost faith in the commission's work.

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.

Hearings were expected to start in March.

In October 2011, President Jacob Zuma announced that Supreme Court of Appeal Judge Seriti would chair the three-man commission of inquiry, assisted by judges Hendrick Musi and Francis Legodi.

Initially, Judge Willem van der Merwe – the same judge who acquitted Zuma on a rape charge – was appointed to help Seriti, alongside Legodi.

However, in December 2011, the presidency said Van der Merwe had indicated he would not be able to serve on the commission, for personal reasons.

Zuma then appointed Free State High Court Judge President Musi to replace Van der Merwe.

In May, commission secretary Mvuseni Ngubane was found dead on the back seat of his car in Pinetown, KwaZulu-Natal. Police said a suicide note was found near the body, but that parts of it were illegible because of blood stains. It was thus not clear why he committed suicide.

As secretary of the commission he would have been responsible for managing its budget and ensuring it had administrative support.

The multi-million rand arms deal has dogged South Africa's politics since it was signed in 1999, after then Pan Africanist Congress MP Patricia de Lille raised allegations of corruption in Parliament.

Zuma was himself charged with corruption after his financial adviser Schabir Shaik, who had a tender to supply part of the requirements, was found to have facilitated a bribe for him from a French arms company.

The charges against Zuma were later dropped.