The midfielder joined Abafana Bes'thende on an 18-month loan deal from Orlando Pirates in January, but after only six months the club released him back to the Buccaneers and immediately stopped paying his salary.
Pirates have also refused to pay Ngobeni, with the Soweto outfit telling the player it is up to him to battle with Arrows for his wages.
Arrows boss Mato Madlala claimed there is a clause in the player's contract that states the club could return him to Pirates at any time, but Ngobeni's business manager Rob Moore says that is not the case.
"The situation is that Clifford signed an 18-month loan contract with Arrows and after six months they have reneged and stopped paying him what they are contractually bound to do so," Moore told The Sowetan.
"Clifford has financial responsibilities, he has a mortgage to pay, and the club have refused to honour their obligations."
The case is set to be heard by the dispute resolution chamber this week.