Djibouti was then effectively told that it would lose its largely self governing status and become a French territory being ruled by the French Parliament. Demands for independence increased after new electoral rules were passed in 1963, effectively abolishing direct representation in the French Parliament in exchange for a system of straight plurality vote based on lists submitted by political parties in seven designated districts within Djibouti. President de Gaulle's visited the territory in 1966 and was left in no doubt about the growing mood for independence and clamours for that change with two days of demonstrations and rioting against a backdrop of many other African nations becoming independent republics throughout the 1960s and early 1970s.

In response to this and following his visit, de Gaulle appointed Louis Saget as Governor General on 21st September 1966 and a further referendum was held to establish the future of the country. When it was held in March 1967 60% voted to remain as part of France and, in July that year, the name of the region was changed to Territoire Francais des Afars et des Issas (the French Territory of Afars and Issas.) The Governor General post was also changed to that of High Commissioner. It should be noted that prior to the referendum 10,000 Somalis were deported from the country with the reason given that they did not have valid identity cards and the result itself was split along ethic lines with the Somali population with its sub-clan of Issas generally supporting independence with a view to joining a united Somalia while the Afar population wanted to remain with France. Interestingly at the time, Djibouti had a population of 58,240 Somali and 48,270 Afar however only 14,689 Somali were allowed to register to vote against 22,004 Afar. There were also suggestions that the French had extended the vote to many Afar living as nomads in Ethiopia. Following the outcome of the referendum there was rioting with the French military killing eleven Issa protestors (below).