Members of the Landlords and Property Owners Association of Washington County had urged their tenants to protest the proposal, which they said is unfair because it punishes all property owners for the misdeeds of a few.
About 15 Landlords and Property Owners Association members protested in front of City Hall before meetings last week and Monday night.
They will protest again at next month's meeting, Association President Alan Johnson said.
Councilman Kristin Aleshire asked that before adopting the ordinance, the council discuss it at a work session next month.
Aleshire also asked for a public hearing on the issue, but no action was taken on that request.
Councilman Lewis Metzner, who cast the only vote against the program, said he has heard much public opposition on the issue.
"A deaf man can hear what the public says about this issue ... I don't know what exactly a public hearing would solve."
At its July 16 meeting, the Hagerstown City Council gave general approval to creation of the program after city officials said it was needed to help the city improve rental housing and prevent people from living in substandard rental units.
Metzner has said he felt the program had changed from one designed to stop substandard conditions to a mechanism to regulate rental businesses. He also has said he thinks it violates citizens' rights to privacy.
Councilwoman Penny May Nigh said a vote against the ordinance would be the equivalent of denying there is a problem with substandard housing.
For the landlords to say they will pass the costs of the fee, and expenses resulting from inspections, on to tenants is "deplorable," Nigh said.
"$45 a year is nothing when landlords are making $500 a month on rental units," she said.
The ordinance exempts the 1,180 rental units owned by the Hagerstown Housing Authority, which are inspected twice a year by the authority.
City Engineer Rodney Tissue said the city's goal is to implement the program next spring.
About 20,000 people in Hagerstown live in rental housing, city officials said.