 He transferred to the South African National Defence Force when MK was incorporated into it in 1994 and he was appointed as major general and served as Deputy General Officer Commanding of Witwatersrand Command in Johannesburg from 1994 to 1996.From 1996 to 1998, Ngwenya was General Officer Commanding of the North West Command in Potchefstroom and from 1998 to the end of September 1999 Chief Director Force Preparation in the Army Office.He served as Deputy Chief of Joint Operations from 1 October 1999 to 31 December 2000.