His appeal to the High Court failed.
The council is now locked in a struggle with the couple to gather correct documentation on the dogs and their ownership, according to a report presented at the council meeting yesterday.
Murray Buchanan, group manager planning and environment, said the council had received "confusing" forms from Mr Phelps' partner Mary Phillips that claimed only one dog still remained in her care.
The forms said dogs that were originally owned by Mr Phelps were now registered to Ms Phillips and some of the animals had died or been sold.
"Without casting aspersions, the dogs have almost disappeared," said Mr Buchanan.
"We're working with her at the moment, trying to identify what happened to the rest of the dogs that were previously in Mr Phelps' name."
He said because of background circumstances with Ms Phillips the council had sent an additional form asking her to provide evidence of the deceased dogs.
"We have been dealing with her very carefully, I don't know if she will comply. She's being co-operative but in no hurry to be co-operative.
"Once we have that information we can go from there."
Mr Buchanan said last year's legal case with Mr Phelps had cost the council more then $10,000 and it was possible there would be further legal action "down the line".
"It's an expensive business for all parties and all for naught. Every other dog owner in the district has complied."
The Times-Age called Ms Phillips to ask her about the situation. When asked what had happened to the dogs, she hung up on the reporter.
