“I pleaded with officers to be tolerant… I even used the Andries Tatane case to show how we can be tolerant in exercising our duties,” Mpembe told the commission.
Tatane died in 2011 when police fired rubber bullets during a protest by residents of Ficksburg in the Free State.
Louis Gumbi, for the family of murdered Warrant Officer Sello Leepaku and wounded Lieutenant Shitumo Solomon Baloyi, said several officers indicated in notebook entries that Mpembe gave instructions to block marching protesters.
The commission is probing the deaths of 44 people in strike-related violence in Marikana, North West, last year.
Thirty four people, almost all striking mineworkers, were killed on August 16 while police tried to disperse and disarm them.
Ten people, including two police officers and two security guards, were killed in the preceding week.
Earlier on Thursday, Gumbi read out notebook entries by three officers dispatched to Marikana on August 13 last year.
Officers were attacked and two were killed, while some were seriously wounded as a result of them blocking the protesters, the officers wrote in their notebooks.
Leepaku and Warrant Officer Tsietsi Monene were shot and hacked to death that day.
Mpembe said the officers omitted some of the vital instructions he issued.
“Regarding these officers put to me as witnesses by Gumbi, none of them indicate that I told them to exercise tolerance,” he said.
“Some mentioned it in their statements, but none wrote it down in their notebooks or diaries.”