A lack of proper evidence showing why Jacob Zuma did not attend his corruption matter led to a warrant of arrest issued against the embattled former head of state.
The warrant has been stayed until May 6 when Zuma is expected to appear again.
In delivering her decision on Zuma's absence, Judge Dhaya Pillay outlined that, while he may indeed be unwell, there was insufficient evidence in court to prove this.
Zuma's lawyer Daniel Mantsha presented the court with a document he said was from a military doctor.
"A military doctor is the person that has been attending to the former president and gave his diagnosis," he submitted.
However, Pillay said there were issues with the document before court. She said that, even though it purported to be a form from a military hospital, there was no other proof provided to her.
She said the form did not say what his condition was and had many points that required clarification that Mantsha could not provide.
"The form says there was a layman's diagnosis with the patient's consent. What does this mean? It is puzzling that there is a reference to a layman's diagnosis, and what the patient is giving consent to is unclear."
She said there were also dates that appeared to be altered.
"The date is altered to be January 6, but there is no initialing of that date. It is not clear that ZK Moteni, who signed this document, is indeed a registered medical practitioner. Mr Mantsha assumes it is his medical practice number. That is guess work."
Senior State advocate Billy Downer said he had contacted Mantsha and his team in January to request details of Zuma's illness.
"My Lady, why are we swimming through mud now? Since January, we have asked for medical evidence and we received no responses from Mr Zuma's team."
Other appeals in the matter
Downer said they had also tried to expedite the appeals process and head to trial earlier, but had hit roadblocks with Zuma's defence.
"As the State, we commenced correspondence with Mantsha and invited them in joining Thales in its direct application to the Constitutional Court. We thought, by doing so, it would cut out appeals in the SCA."
Mantsha, however, added that it was within Zuma's rights to pursue any appeals process.
"My client is within his rights. He also feels his issues are different from that of Thales."
Zuma has petitioned the SCA for leave to appeal the dismissal of his application for a permanent stay of prosecution.
He argued in court papers that he is being used as a "scapegoat" in the corruption case against him.
He also said the State should have investigated those who were closer to decision-making at the time, including former president Thabo Mbeki.
The matter returns to court on May 6.