As part of the deal that brought Fowler to City last January, the Yorkshire club agreed to pay him around £10,000 each week - on top of the £40,000 he is earning from his new employers.
However, that extra payment has now been axed as Leeds seek to gather enough cash to stave off administration.
City have no cause to complain to the authorities though as it was a private agreement.
A City spokesman said: "Any arrangement between Robbie Fowler and Leeds is the responsibility of those two parties and we can't comment."