Former president Jacob Zuma's son Edward has accused the high court judge who issued a warrant for his father's arrest of bias, saying she is close friends with two of his political foes.

The younger Zuma said in an interview on television news channel eNCA Judge Dhaya Pillay was friends with public enterprises minister Pravin Gordhan as well as former cabinet minister and ruling African National Congress (ANC) veteran Derek Hanekom.

"These are family friends who've known each other for years," he said, adding that he was sure when they socialised, they might discuss "some issues".

At the Pietermaritzburg High Court on Tuesday, Pillay issued a warrant of arrest for the former president after he failed to appear for his graft case. His lawyer produced a medical certificate from a military doctor that the State argued was not valid.

The warrant will however not be executed unless Zuma fails to show up at court for his next scheduled appearance on May 6.

He is due to go on trial for allegedly taking bribes from French arms manufacturer Thales, through his former financial adviser, when South African negotiated a big arms deal in the late 1990s.

Zuma's son said there were people within the ANC intent on destroying his father's political legacy.