Stefan Trpcevski, 35, has pleaded guilty to 99 charges and is currently before the ACT Magistrates Court.

Authorities previously said they found 27 dogs in varying states of neglect when they raided two properties in Macquarie and Ainslie late in 2013.

Trpcevski was charged with numerous offences ranging from failing to provide animals with adequate food and water, to failure to seek veterinary treatment and keeping dogs that were unregistered or not de-sexed.

Vets at the RSPCA shelter in Weston, who assessed several animals seized from the Ainslie home at the time, spoke of the animals' poor health during a sentencing hearing on Monday.

Former RSPCA vet Ashley Jordan told the court one of the dogs, "Bindy", was underweight, suffered hair loss and had fly bites and scabs on her head.

He said the dog was assessed as a three out of nine on the body condition scoring chart used to calculate body fat levels, with one being emaciated and nine being obese, and the likely reason for her low weight was that she had been underfed.

Under cross-examination, Dr Jordan said while it would be possible for the dog to be bitten several times without an owner noticing, it shouldn't be difficult to prevent ongoing fly bites before they got that severe.

The court heard vets assessed another male crossbreed dog as one, or emaciated, on the body condition scoring chart, as the animal's hip bones and spine were clearly visible.

Prosecutor Katrina McKenzie told the court the "unnecessary pain" caused to the animals in Trpcevski's care was such that a term of imprisonment should be imposed.

Trpcevski's defence lawyer told the court her client suffered from debilitating mental illness, which impaired his judgment, and he had been receiving help from ACT Mental Health.

Chief Magistrate Lorraine Walker ordered a pre-sentence report be prepared before the matter returns to court for sentencing in March.