I had been researching the histories of the DC-3s I photographed on a visit in Nov. 2005 to Australia. Frequently I came across references of civil registrations used for military aircraft. When reading about the individual histories of the aircraft I noticed military registrations were always accompanied by civil regs, sometimes recorded with a hyphen or not (VHRFS or VH-RFS) and sometimes with a strange prefix (VMMKS); I vaguely remembered these were used as radio callsigns.
So I posted a question about this on the Yahoo Oz-spotters forum.
The answers have been reproduced below.
You are on the right track with the idea of radio call signs.
Aircraft registration nationality letters are a sub-set of the radio callsign nationality letters allocated to each company. The radio call signs are allocated now by the International Telecommunications Union, ITU, which is a UN body. They used to be allocated by the CCIR which stands for something in French (something like Committee Consulatif Internationale Radio......., not sure of the last word and radio is not my specialist branch of communications).
The tie up of aircraft nationality letters and radio call signs occurred in 1929 and this is why there was a major change to aircraft marks in that year. e.g. The UK went from K to G-, Nederlands from H-N to PH-, Australia from G-AU to VH- etc. There are not many places in the world these days that you hear radio callsigns used other than for amateurs. The USA is one, all their radio and TV stations use their call sign, e.g WNBC or KABC (W are west coast stations and K east coast).
http://www.ac6v.com/prefixes.htm gives the allocations but is focused on amateur radio but it has links to a number of other relevant sites, one of which lists the radio allocations with an aviation focus. I haven't checked this 2nd list but I have seen a number of aviation related ones that have many errors in them particularly with understanding the independence of the many ex-colonies of various European nations. One used to be available on the Landings site.
You will see from this that Australia is allocated VHA to VNZ, AX and VZ. VM is now for commercial stations but used to be used for military callsigns.
One standard I've adopted in my records, to distinguish the Service Radio Call Signs from Civl Registrations is to shew them as VHC-xx, i.e., for the Lodestar flown by Qantas under A.D.A.T., VHC-AA, etc.
An interesting point is that when the Dutch in the Netherlands East Indies handed over to the Indonesians, their Dakotas, which had used VHR-xx Call Signs during the War, became PK-Rxx, with the same last two letters.
When I first came to OZ in 1967 RAAF transports used radio call signs.
The C-130As were in the VM-JL series
The C-130Es VM-NU
The Caribous VM-JM