1. Introduction

Only the Navy Headquarters can be identified by their callsigns. This is not the case for all other stations; the HQs do communicate with a multitude of stations which are on ships or are land based for supplies, logistics, training or coastal defense.
We are monitoring Morse networks, which, to a great part, are for training and backup purpose. Since many years the same callsigns are used, but that doesn't necessarely mean they are used on the same station. I do not think the Navy has any interest to reveal their structure - not even for training networks. Long-time monitoring of the same frequencies proves, that one operator handles more than one callsign; this becomes obvious, when his keying is easely recognised and when he mixes up callsigns.
Only Radio Direction Finding with professional equipment can bring us further. Experiments with a Crossed-Loop - and Magnetic Loop Antenna have started, but there is still a long way to go. More about my RDF possibilities here: Radio Direction Finding .

A spreadsheet with CIS Navy callsigns/traffic can be downloaded here: Downloads
If you know more about the allocation of Navy callsigns please let me know.

The Navy callsigns have the following formats (L = letter, F = figure):

2. Allocation of Callsigns

From  To  User 
RAL  RML  High ranking, HQ or collective callsigns 
RALL  RMLL  Individual or collective callsigns, fix or mobile.  
RALFF  RMLFF  Individual or collective callsigns, fix or mobile 
FFFFF     Aircraft of the Naval Air Transport Unit 
WLHN    Collective callsign, to (all?) units of the Armed Forces.  

3. Special Purpose Callsigns

There is a series of call signs which are used for a certain purpose or by certain stations.

Naval Air Transport
Aircrafts always use 5-figure call signs, which are not re-used. An aircraft or a route cannot be identified by the call sign. More here: Naval Air Transport Units .

Collective call signs
Certain collective call signs do not stand for a fleet or a task force, but for an area.
Navigational -/Gale Warnings from Sevastopol to RGX94 always concern French Waters, such to RBE86 the Ionian Sea, Tunesia and the Syrte,such to RIP90 concern Turkish Waters and the Aegeis and to RKZ the Mediterranean Sea. Kaliningrad transmits to REO the Baltic Sea State and Severomorsk to RLO North Sea conditions. Be aware, that, in certain cases, all HQ issue warnings to any collective callsign.


The RJxxx Series call signs
There is a series of callsigns, which do not answer on the primary frequencies 8345 and 12464 kHz and they can be found in simplex mode on a frequency out of a pool; the busiest being 8120, 8128, 10796 and 13469 kHz.
The following, and for sure many more, are concerned:
RJC66
RJD25, RJD35, RJD36, RJD38, RJD46, RJD52, RJD69, RJD71, RJD77, RJD80, RJD85, RJD87, RJD99
RJE56, RJE58, RJE65, RJE67
RJF48, RJF95, RJF96
RJH25, RJH41, RJH57, RJH63, RJH69, RJH77, RJH90.

RJE56 always is the NCS, it is operated by Ny HQ Moscow. This becomes obvious, when the operater in error uses RIW and then changes to RJE56.

RJH45, RJD38, RJF41, RJE73, RJH74
These callsigns seem to be used in connection with the Navys Hydrographic Service. If ships transmit Sea State and Weather Data in WMO FM-13 format to their HQ, these callsigns are the addressees.

Example:
RCV de RCJG QTC 517 ..... = sml for RJH45 RJH74 = 23121 99362 70007 ... k

These messages are interesting, because they do contain position reports in groups 2 and 3.