Union leaders noted that suspects had suffered serious injuries while riding in the Ford cargo vans.
"We never had [an officer] seriously hurt, but it was only a matter of time," union president Richard B. Costello said.
In 1998, the city spent $343,000 to buy nine passenger vans with padded seats and seat belts to shuttle officers around.
When circumstances require moving more officers than can fit in those vans, the department still avoids using wagons. During the Republican National Convention last summer, officers were transported in vehicles borrowed from the Sheriff's Department.
To this day, the Police Department transports suspects in the old wagons, which have no seat belts or protective padding. Suspects sit on low, hard, fiberglass benches and ride with their hands cuffed behind them, adding to the risk of injury.
Though officers rode in the wagons with their hands free, "it is extremely uncomfortable and, more importantly, unsafe," Costello said. "There's nothing to hold on to. We've had people bounced around."
When department brass began planning the purchase of the new passenger vans, the idea was that officers and prisoners alike would ride in them.
But when the new vans hit the street, the plan had changed: They were for police only.
Costello said he could not understand why the department continued to put prisoners in vehicles with a demonstrated potential for harm.
"It's my job to worry about my troops," he said. "But as a police officer, I have to worry about the safety of those in our custody. Because nobody knows better than us they're not all guilty."