"The foundation or cornerstone for the development of all geopolitical data standards was the approval of a standard for country identification within the Department of Defense in October 1969. This standard has since evolved into a Federal General Data Standard as promulgated in Federal Information Processing Standards Publication (FIPS Pub 10), 15 June 1970." -- Geopolitical Data Elements and Related Features, Defense Intelligence Agency, Washington, 1972-09-29.
FIPS PUB 10 was first published in 1970. It included two-letter codes for countries, and codes for primary administrative subdivisions of countries that consisted of the applicable two-letter country code with two digits appended. (In later editions, the appended characters were allowed to be letters if needed.) It has been modified over the years, and updated with new editions in 1974, 1976, 1984, and 1995. The updates are designated FIPS PUB 10-1, 10-2, 10-3, and 10-4 respectively. They have been maintained by the National Geospatial-Intelligence Agency (NGA).
The ISO country code standard was introduced in 1974. This put U.S. government agencies on the horns of a dilemma. Should they use FIPS codes and follow the domestic standard, or switch to ISO codes for a more international approach? I was told that the Departments of State and Defense used FIPS codes, while government agencies dealing with international trade and cooperation used ISO Alpha-2 codes. The ISO standard was given a FIPS number (FIPS PUB 104-1, withdrawn on 1997-07-29). Both sets of codes were entrenched in their respective spheres. (Source  alludes to the confusion and contains plans for resolving it.)
On 2008-09-02, FIPS PUB 10-4 was withdrawn. The standard will eventually be phased out entirely and replaced with one that is closely synchronized with ISO 3166-2. The NGA was not ready to switch over immediately. It continues to maintain the code set, but no longer as a federal standard. The successor standard to FIPS 10-4 is titled "Geopolitical Entities and Codes" (GEC for short). The NGA site has links to more information.
After a short delay (on the bureaucratic time scale), a new federal standard was issued. Its name is "Geopolitical Entities, Names, and Codes" (GENC for short). GEC and GENC are standards that denote the same things by different codes. GENC Edition 1 was published on 2012-09-01. It was closely based on ISO 3166-1. It used the same two-letter country codes as ISO wherever possible, and it didn't provide subdivision codes. An Edition 2 followed on 2014-03-31, extending the first edition with subdivision codes. If I understand the situation, GEC will phase out in a few years and will be entirely superseded by GENC. I have not yet found out how the government plans to maintain GENC.
Like ISO 3166-2, GENC provides primary subdivision codes at two different levels for some countries. For example, it has codes for both the autonomous communities and the provinces of Spain. GENC identifies the "Subdivision Category" of each one, so they can be told apart, but I can find nothing in the standard that tells me that they overlap—for example, that Badajoz and Cáceres provinces are the same territory as Extremadura autonomous community.
The NSG standards registry gives more details about GENC.
The following timeline lists all the changes I could find that have affected the names or the codes for any country. In most cases I haven't mentioned the code values following a change, because they can be looked up in the Country Codes table, or sometimes farther down the timeline. When the note says that country A split from country B, it means that country B's FIPS code did not change, unless its previous code is specified.
CL) merged with Gilbert and Ellice Islands; name of Ceylon changed to Sri Lanka; name of Cocos Islands changed to Cocos (Keeling) Islands; name of Congo (Brazzaville) changed to Congo; name of Congo (Kinshasa) changed to Zaire; name of Communist China changed to Peoples Republic of China; Coral Sea Islands Territory split from Australia; name of Falkland Islands changed to Falkland Islands (Islas Malvinas); name of Heard and McDonald Islands changed to Heard Island and McDonald Islands; name of Muscat and Oman changed to Oman; name of Papua and New Guinea changed to Papua New Guinea; Southern Ryukyu Islands (
YQ) merged with Japan; name of Southern Yemen changed to Yemen (Aden); name of Soviet Zone of Germany changed to German Democratic Republic; name of Spanish Territories in Northern Morocco changed to Spanish North Africa; name of Spratly Island changed to Spratly Islands; Swan Islands (
SQ) merged with Honduras; name of Trucial States changed to United Arab Emirates; name of United Arab Republic changed to Egypt; name of United States Misc. Caribbean Islands (
BQ) changed to Navassa Island, as a result of several minor islands being transferred from the U.S. to Colombia; name of West Berlin changed to "Germany, Berlin"; name of Yemen changed to Yemen (San'a).
SK) merged with India, according to FIPS 10-1 Change Notice No. 4.
GN) split into Gilbert Islands (
GS) and Tuvalu, according to FIPS 10-1 Change Notice No. 11.
DM) changed to Benin, according to FIPS 10-1 Change Notice No. 12.
VN) and Republic of Viet-Nam (
VS) merged to form Vietnam, according to FIPS 10-1 Change Notice No. 14.
PT) merged with Indonesia, according to FIPS 10-1 Change Notice No. 15.
WB) to (
BZ); Israel-Jordan Demilitarized Zone (
IW) and Israel-Syria Demilitarized Zone (
IU) merged with Israel; Jan Mayen and Svalbard merged to form Svalbard and Jan Mayen (
JS); name of North Korea changed to Democratic People's Republic of Korea; name of Pitcairn Island changed to Pitcairn; name of Republic of China changed to China (Taiwan); name of South-West Africa changed to Namibia; name of Soviet Union changed to Union of Soviet Socialist Republics; Spanish North Africa (
ME) merged with Spain; name and code of Spanish Sahara (
SS) changed to Western Sahara (
WI); name of Tanzania changed to United Republic of Tanzania; name of Virgin Islands changed to Virgin Islands of the U.S.
FT) changed to Djibouti (
DJ), following the country's independence on 1977-06-27, according to FIPS 10-2 Change Notice No. 1.
CQ) split from Trust Territory of the Pacific Islands (
TQbefore the change), according to FIPS 10-2 Change Notice No. 3.
EQ) and Gilbert Islands (
GS) merged to form Kiribati, following the country's independence on 1979-07-12; name of Central African Empire changed to Central African Republic; Canal Zone (
PQ) merged with Panama, with no change to the latter's name or code; name of Saint Vincent changed to Saint Vincent and the Grenadines, following the country's independence on 1979-10-27, according to FIPS 10-2 Change Notice No. 7.
RH) changed to Zimbabwe (
ZI), following the country's independence on 1980-04-18, according to FIPS 10-2 Change Notice No. 8.
PM, in a belated reflection of the Canal Zone merger, according to FIPS 10-2 Change Notice No. 9.
YE) changed to Yemen (Sanaa), according to FIPS 10-2 Change Notice No. 11.
IQ) split into Baker Island, Howland Island, Jarvis Island, Kingman Reef, Palmyra Atoll; Bassas da India, Europa Island, Glorioso Islands, Juan de Nova Island, and Tromelin Island split from Reunion; name of Republic of Cape Verde changed to Cape Verde; name of China (Taiwan) changed to Taiwan; Clipperton Island split from French Polynesia; Guernsey, Isle of Man, and Jersey split from United Kingdom; Svalbard and Jan Mayen (
JS) split into Jan Mayen and Svalbard; Mayotte split from France; name of Virgin Islands of the U.S. changed to Virgin Islands, according to FIPS 10-2 Change Notice No. 12.
BN, according to FIPS 10-2 Change Notice No. 13.
NQbefore the change), according to FIPS 10-3 Change Notice No. 6.
GC), "Germany, Berlin" (
BZ), and Federal Republic of Germany (
GE) merged to form Germany (
GM); Yemen (Aden) (
YS) and Yemen (Sanaa) (
YE) merged to form Yemen (
YM), according to FIPS 10-3 Change Notice No. 8.
FA) split into Falkland Islands (Islas Malvinas) (
FK) and South Georgia and the South Sandwich Islands; code for Netherlands Antilles changed from
NT, according to FIPS 10-3 Change Notice No. 9.
UR), according to FIPS 10-3 Change Notice No. 10.
UR) split into Armenia, Azerbaijan, Byelarus, Georgia, Kazakhstan, Kyrgyzstan, Moldova, Russia, Tajikistan, Turkmenistan, Ukraine, and Uzbekistan, according to FIPS 10-3 Change Notice No. 11.
YO) split into Bosnia and Hercegovina, Croatia, Macedonia, Montenegro (
MW), Serbia (
SR), and Slovenia, according to FIPS 10-3 Change Notice No. 12.
IY) divided between Iraq and Saudi Arabia, according to FIPS 10-3 Change Notice No. 13.
CZ) split into Czech Republic and Slovakia; name of Ivory Coast changed to Côte d'Ivoire, according to FIPS 10-3 Change Notice No. 14.
TC) to (
AE); name of Western Samoa changed to Samoa; name of Zaire changed to Democratic Republic of the Congo, according to FIPS 10-4 Change Notice No. 1.
MW) and Serbia (
SR) merged to form Yugoslavia (
YI), according to FIPS 10-4 Change Notice No. 6.
YI) split into two countries, according to FIPS 10-4 Change Notice No. 11.
AX), Dhekelia Sovereign Base Area (
DX), Etorofu, Habomai, Kunashiri and Shikotan Islands (
PJ), Undesignated Sovereignty (
UU). The first two are British military bases in Cyprus. The third is a territory administered by Russia and claimed by Japan. The fourth encompasses the third, as well as the Spratly and Paracel Islands. This update was reported in FIPS 10-4 Change Notice No. 12.
RI, and code
KVissued for Kosovo, according to FIPS 10-4 Change Notice No. 14. The code for Kosovo was actually assigned in February.
DXchanged to Akrotiri and Dhekelia, respectively, according to Update 1.
NT) split into three parts, of which two were assigned country codes: Curaçao (
UC) and Sint Maarten (
NN), according to Update 2. The remainder became part of the Netherlands.
SU. South Sudan became
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