I believe even the Civil XPDRs use IFF.
IFF is still in use by both military and civilian aircraft. Modes 1, 2, 3, 4 and 5 are for military use only. Modes 1, 2 and 3 are collectively known as Selective Identification Feature (SIF) modes. Civilian aircraft use modes A, C and S. Mode C which includes barometric pressure altitude information is often used in conjunction with Mode A. Mode A is often referred to as mode 3/A due to the similarity to the military Mode 3. Mode S is a new civilian mode developed to replace both Mode A and C.
This is from
Identification friend or foe - Wikipedia, the free encyclopedia
That was what happened in the Iran Air Shootdown when it was wrongly identified as a hostile..
The short distance made for a simple flight pattern: climb to 14,000 feet (4,300 m), cruise for a short time, and descend into Dubai. The airliner was transmitting a friend-or-foe identification code for a civilian aircraft and maintained English-speaking radio contact to civil flight control.
More here.
Iran Air Flight 655 - Wikipedia, the free encyclopedia
Cheers