Lt Gen Shadrack Sibiya, who was detained on Monday, made no comment during his court appearance. He is also facing a charge of trafficking, which prosecutors say could lead to further arrests. The 59-year-old is due to appear in court again on 29 September for a bail application, which prosecutors are expected to oppose.
The state has requested a change in the prison where Sibiya is held, citing indications of a potential escape plan, according to national broadcaster SABC.
The charges come as the South African police service faces intense scrutiny at a major public inquiry, the Madlanga Commission, which began last September. The inquiry has heard allegations that Sibiya received a gift of 20 impalas from an alleged criminal kingpin in exchange for a police contract — accusations he has denied.