South Africa's police boss has put his deputy on "leave of absence" as part of an investigation into allegations of links between suspended Police Minister Senzo Mchunu and organised crime groups.

It comes after President Cyril Ramaphosa had on Sunday suspended his police minister who was linked to criminal syndicates with ties to drug cartels. The president also announced a judicial commission of inquiry to investigate the claims.

The suspended minister has denied wrongdoing and said he supported the president's decision.

National Police Commissioner Fannie Masemola said on Tuesday that his deputy and head of crime detection, Shadrack Sibiya, had been instructed “to stay at home” pending investigations.

‘Disturbed and surprised’

But in response, Sibiya said he was "a little bit disturbed and surprised" by the decision, the public broadcaster SABC reports.

"I’ve got a legal team that is supporting me. It’s my wish for everybody who’s involved to allow the process as announced by the president to take its natural course,” he is quoted as saying.

The corruption allegations emerged last week after Lt. Gen. Nhlanhla Mkhwanazi, a provincial commissioner in KwaZulu-Natal, told a media briefing that Mchunu and other top police officials were linked to criminal syndicates with ties to drug cartels.

He claimed that Mchunu had allegedly interfered with sensitive police investigations including the disbanding of a police unit tasked with investigating politically motivated killings to shield politicians, police officers and other people involved in the crimes.

President Ramaphosa said the allegations made by Mkhwanazi raised serious concerns around the constitution, the rule of law and national security.