City officials won't say why Oscar Perez, shelter manager since 2015, has been put on leave.
Shelter volunteers say the facility has made a lot of progress in reducing euthanasia in recent years and they are concerned a change in management could hinder those efforts.
One volunteer said after Perez was escorted out of the facility, his replacement immediately had 11 dogs euthanized.
The city said the animals were either too violent or were past the date for when they needed to be adopted.
But some volunteers say the animals were healthy and there were empty kennels still available.
City manager Andrea Miller says the facility hasn't been properly invested in over recent years as the city comes out of a bankruptcy.
"The facility is obsolete, and like many of our facilities we realize it needs a major infusion of investment," she said.