Ngobeni moved to Golden Arrows on an 18 month loan from Orlando Pirates in January.
However, the Durban-based side now claims to have offloaded the midfielder from their ranks and refuse to pay Ngobeni's salary and part of the signing on fee of around R500 000.
Ngobeni is reportedly claiming about R1.3 million as compensation from Golden Arrows, who have not been paying his salary since May.
In their defence, Arrows maintain that a clause in Ngobeni's contract empowers them to return the player to Pirates if they wish to do so.
However, Orlando Pirates spokesperson Mickey Modisane is distancing his club from the saga.
"As far as we are concerned this matter involves Ngobeni and Arrows. Clifford is contracted with the club so they are the ones who are dealing with the matter," says Modisane.
Ngobeni – who rose to prominence while still at Ajax Cape Town in 2007 and 2008 – has failed live up to expectations, struggling to settle at both Pirates and Arrows.
Ngobeni, who is now struggling to pay his debts and provide for his family, is eager for the case to be finalised.