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"Four armed men entered metro police head Eugene Nzama's residence and held two of his security guards, who were on duty, at gunpoint on Wednesday at about 6pm," Colonel Vincent Mdunge said.
Mdunge said the robbers disarmed the security guards and shot them before fleeing.
One of the guards was in a critical condition in hospital. The other's condition was stable.
Nzama and his family were not at home at the time of the shooting.
"It is unclear what the motive for the shooting was, but our investigations will establish that," Mdunge said.
Police are investigating a case of armed robbery and attempted murder.
In recent months the Durban metro police have staged protests demanding Nzama's removal from his position because they were unhappy with his management style.
He was put on special leave in July before the Durban Labour Court allowed him to resume duty.