The Greek Orthodox of Crete, who made up two-thirds of the island's population, had revolted many times against their Ottoman rulers, most recently in 1866 and 1878. In response to the 1878 revolt and pressure from the Powers at the Congress of Berlin, the Ottomans had instituted the Halepa (Chalepa) Pact, granting Crete a limited amount of self-government: a Christian was to be governor, an assembly (forty-nine Christians and thirty-one Muslims) was elected, a local gendarmerie created, Greek, as well as Turkish, was made an official language of the courts and the assembly, Greek officials were selected by the Greeks for provincial administration, taxes were reduced and half of the island's customs were allocated to the provincial government. In effect, Crete was granted a certain degree of autonomy, more than other Ottoman provinces.

The Halepa system was less than successful. It did not greatly reduce tensions on Crete or opposition to Ottoman rule. Finances became a shambles. Conflicts arose in the Assembly among political parties and between politicians and the governor. A new revolt broke out in 1889. It quickly dissolved into inter-communal warfare between Christians and Muslims. In 1889, Sultan Abdülhamid II restricted the Halepa Pact. Most of the prerogatives of the Assembly were abrogated. Martial law was declared, and the rebellion was put down. All customs receipts were sent to Istanbul, leaving all finances under Central Government control and ending any financial autonomy. From that point, the Ottoman governor alone ruled Crete.

Beginning slowly in 1895, increasing in 1896 and dissolving into a total civil war in 1897, Greeks in Crete revolted against the Ottoman Government. Their stated intention was union (enosis) with Greece. It became a two-fold war – Greek rebels against Ottoman troops and intercommunal war between Christians and Muslims, in which each side engaged in massacres of the other. The Greeks, in greater numbers and well supplied with weapons from Greece, had the upper hand. Ottoman troops, scattered across the island, were too few to effectively intervene. The troops concentrated in coastal fortifications. Muslims in the interior, unprotected, fled to the coasts; Greeks from the coasts fled to the interior.