Being labelled undeployable means the officer can't leave the station, or interact with members of the public, until they've passed the fitness test.
Police national manager for wellness and safety Marty Fox said the move was "nothing to do with fitness" of officers, but more about consistency of rules.
He believed the changes wouldn't lead to a drop in front line staff.
"What we're seeing is very small numbers going past the due date now.
"With our level one responders, there are 8000, but the numbers going past the due date are under 100."
Police bosses didn't have any evidence on whether that number would increase under the tougher fitness stance, Fox said.
But Police Association president Chris Cahill said the changes would put a "big strain" on resources and staffing.
"Some of these teams can be quite small, and the loss of even one member that's stood down can make a real strain for the other staff, or even make the teams dysfunctional.
"At times they won't meet minimum staffing levels, so it creates safety issues."
The organisation was entitled to make sure all officers were up to the job, he said.
But many of the officers currently unable to sit a fitness test were dealing with a small injury, that didn't stop them completing their work duties.
The Police Association wants Police headquarters to allow more flexibility, or at least ensure there's enough staff to fill the gaps.
"There isn't necessarily staff from backroom jobs who can go fill those, especially because not everyone is trained to be able to go from one role to another.
"I certainly think we need to look at what effect it's having on staffing numbers, especially those front line staffing numbers.
"If it's creating significant pressure, we need to consider extra staff."
Fitness tests are held at regular intervals, but many officers say it can take a long time to arrange one that works with the variety of shifts they are expected to work.