Lisa Caldwell, 21, was charged with mistreating the dog after being visited by officers at her home in Pennywell Gardens.
Bosses at the sanctuary in Seafield Road East said the charges were "most disturbing" and, "if true, it's completely unacceptable".
Caldwell, who has worked at the facility for around six months, was reported to the police on January 10. When officers visited her ground-floor home four days later, she was charged with the offences.
Her neighbours said she owned a German shepherd and a cat.
Caldwell pleaded not guilty during an appearance at Edinburgh Sheriff Court on February 18 to two charges under the Animal Health and Welfare (Scotland) Act 2006. She was accused of "causing a protected animal unnecessary suffering by act or emission" and "failing to meet the needs of a protected animal".
David Ewing, manager of the Seafield home, said: "We're aware of this court case. She has been suspended from the time we discovered this was going on, and we're now waiting for the outcome of this case.
"It will then be passed to our board of trustees if she is found guilty, and it will be for them to decide what action is taken.
"We took these steps from the time she was charged, and we're now waiting to hear the full circumstances.
"She's a young woman who has not been with us for very long, more than a few months, but not long. She was a kennel worker.
"Clearly this is a concern to us, and we've taken prompt action to deal with it.
"It's something that is most disturbing, and if it's true then it's completely unacceptable."
A police spokesman said: "A 21-year-old woman was charged in relation to the mistreatment of an animal.
"A report has been sent to the procurator fiscal."
A Crown Office spokeswoman confirmed that Caldwell had appeared in court to face the charges.
She added that an intermediate diet had been set for March 11, with a trial scheduled at Edinburgh Sheriff Court for March 26.
Caldwell could not be reached for comment.
HOW THE LAW CAN STEP IN TO HELP
The Animal Health and Welfare (Scotland) Act was passed in a bid to tackle animal cruelty and means owners of animals have to ensure welfare standards.
Prior to the Act, owners only had a duty to ensure that an animal did not suffer unnecessarily. The new Act imposes a broader duty of care to take reasonable steps to ensure that the animal's needs are met.
These include providing a suitable living environment and diet, and protecting animals from pain, suffering, injury and disease.
Offenders can be fined, sent to prison, have their animals taken away, and disqualified from keeping pets in the future.
The maximum penalty is imprisonment for up to 51 weeks, or a fine of up to 20,000, or both.