Encrypted messages are a form of Chest Loot that you can acquire by Killing Faction Scouts. Faction Scouts are Interceptors that move much faster than the normal system hostiles, and as such are easily recognizable at a glance through the system. The amount of Messages you can receive is based on the Scout level (note, it is possible to kill a Scout and receive 0 messages). Encrypted messages can then be redeemed in the Faction store for Faction Credits. As you rank higher in reputation, both the Cost of the Message Exchange Chest and the Reward in the Message exchange chest, increase.

• To Recieve Federation credits, you must kill Kingon Scouts, and receive Klingon Messages.
• To Recieve Romulan credits, you must kill Federation Scouts, and receive Federation Messages.
• To Recieve Klingon credits, you must kill Romulan Scouts, and receive Romulan Messages.

Federation Scouts are Found in Federation Space 
Siiolux (35) Warp: 24
Tau Ceti (34) Warp: 25
Aiti (33) Warp: 26
Thama (32) Warp: 27
Andoria (34) Warp: 30
Sirius (36) Warp: 38
Wolf (39) Warp: 40
Archer (36) Warp: 45
Tellar (37) Warp: 47
Deneb (38) Warp: 47
Zosam (40) Warp: 64
Goesting (40) Warp: 65
Hyland (42) Warp: 70
Kildare (43) Warp: 75
Rua Ri (42) Warp: 75
Almango (43) Warp: 75
Jera (44) Warp: 95
ST-9417 (45) Warp: 110
Leebyrn (46) Warp: 120
Ertalwu (47) Warp: 120
Enten (45) Warp: 120
Yarega (47) Warp: 135
Caelum (49) Warp: 160
Miers (49) Warp: 160
Rylan (50) Warp: 185
Agataylor (52) Warp: 230
Bairbre (54) Warp: 285
Areal (56) Warp: 355
X6-094 (58) Warp: 440

Romulan Scouts are found in Romulan Space
Unroth (32) Warp: 26
Kaisu (33) Warp: 26
Aesir (34) Warp: 30
Nequencia (38) Warp: 30
Vendor (34) Warp: 32
Altanea (38) Warp: 38
Alpha Onias (36) Warp: 38
Iapedes (36) Warp: 38
Terminimurus (39) Warp: 40
Rowla (40) Warp: 64
Tolain (40) Warp: 65
Delmas (42) Warp: 70
Ami Bera (43) Warp: 75
Talvath (43) Warp: 75
Corvidae (42) Warp: 75
Ril Korvas (44) Warp: 95
Naalur (44) Warp: 110
Elvros (47) Warp: 120
Nuva (45) Warp: 120
Ballion (46) Warp: 120
Urhaasi (47) Warp: 135
Loch'Grman (49) Warp: 160
Jorda (49) Warp: 160
Aralen (50) Warp: 185
Magnus (52) Warp: 230
Mons Mortis (54) Warp: 285
Kalalisko (56) Warp: 355
Dairuum (58) Warp: 440

Klingon Scouts are found in Klingon Space
Eeli (33) Warp: 27
Lixar (35) Warp: 28
Forseti (36) Warp: 30
Ok'Vak (32) Warp: 31
Beta Penthe (34) Warp: 33
Quv Qeb (36) Warp: 38
Gorath (38) Warp: 39
Mempa (38) Warp: 39
Brestant (39) Warp: 40
Gya'han (39) Warp: 40
Ja'Corash (40) Warp: 64
Garyb (40) Warp: 65
B'Oh (42) Warp: 70
Klopp (42) Warp: 75
Toh'Kaht (43) Warp: 75
Inocula (43) Warp: 75
Somraw (44) Warp: 95
Het'Tenz'A (45) Warp: 110
nuHmey veQ (45) Warp: 120
Annalu (47) Warp: 120
Erzon'Uk (46) Warp: 120
Ch'Kmulk (47) Warp: 135
Rai'Trohk (49) Warp: 160
Nalla (49) Warp: 160
Inoss (50) Warp: 185
Ariadexa (52) Warp: 230
Santesso (54) Warp: 285
Kur'than (56) Warp: 400
Atlhe (58) Warp: 440