Eh. Military aircraft would also have a transponder, they just wouldn't necessarily have active broadcasts.

Civilian aircraft do broadcast actively (ADS-B). But they also respond to secondary radar for Mode A/C, which are basically cases of IFF Mode III (okay, maybe not exact term, but the idea applies.) So it's still a challenge-response/IFF, just in this case always responding.

Military aircraft use different modes and presumably don't respond unless interrogated with an appropriate challenge, but the principles are the same.