South Africa's deputy police chief has resigned amid charges of sexual offences and corruption, three weeks after his arrest.

Lieutenant General Shadrack Sibiya, 59, had been due to face a disciplinary hearing on Monday. His lawyer submitted a resignation letter at the start of proceedings, a police spokesperson confirmed.

Police spokesperson Athlenda Mathe said in a post on X that Sibiya's departure from the force was regarded as a "dishonourable discharge" because he resigned while a disciplinary case against him was still ongoing.

Sibiya has been in custody since his arrest last month. His application for bail has been postponed to October 13.

He faces charges of sexually grooming a 16-year-old girl, raping an 18-year-old woman, and human trafficking. He denies the rape and grooming allegations, but acknowledges he had sex with the 18-year-old, saying it was consensual.

Sibiya had been suspended since September last year, following allegations that emerged at a major public inquiry into police corruption and alleged ties to organised crime, known as the Madlanga Commission.

At the commission, Sibiya was accused of interfering with investigations into political killings in KwaZulu-Natal province. He was also accused of receiving large sums of cash, as well as 20 impalas, from an alleged criminal kingpin in exchange for a police contract. He denied those allegations during his testimony.

The Madlanga Commission was established by President Cyril Ramaphosa after the KwaZulu-Natal police chief held a press briefing in which he accused the then Police Minister Senzo Mchunu of working with criminal gangs.

Mchunu denies the allegations against him but has also been suspended.

The commission has drawn widespread public attention over the past year, unearthing extensive allegations of links between senior police officers and crime bosses.