Employees were ordered to turn over all handguns, rifles, shotguns and ammunition to the LAPD. Police will hold onto the weapons until the audit is done.
Officials said the weapons were being used to euthanize injured wildlife in a humane way.
City Controller Wendy Gruel said there is a lack of appropriate internal controls over the use of weapons at the shelters.
She added that more needs to be done to find out how many weapons there are and how they're being used.