Pirates announced their 31-man squad for the coming season yesterday, but Ngobeni's name was not on the list – despite him still having a two-year contract with the double treble champions.
However, the former Ajax Cape Town midfielder tells KickOff.com that he is no longer training with the club.
"I was told at the beginning of the month that I must stop training with the team," he says.
"Since then I have been training alone and I don't know what will happen as I'm still waiting for the club to tell me what will happen with my future."
Ngobeni was on loan at Golden Arrows last season, but was recalled by Pirates at the end of the season.