It was the inability of the Ottoman navy to provide security of passage for the reinforcement and supply of troops during the ultimately successful Ottoman campaign to capture the island of Crete that finally led to a reinvigoration of the imperial navy and its adoption of sail over oar. Known as the fifth Ottoman-Venetian War, or sometimes the Cretan War, the conflict broke out in 1645, with the popular version of its cause relating to a squadron of six galleys belonging to the Knights of St John capturing and towing in to the Cretan port of Chania an Ottoman galleon bound for Mecca. Among those on board the captured vessel, so it was said, were a number of women bound for the seraglio and possibly also a child of the Sultan. In having put into Crete, the Knights gave to Bernardo Morosini, the Venetian-appointed Governor of the island, gifts taken from the galleon, including some fine Arabian horses. In the words of Kâtip Çelebi (1609–57), ‘the ruler of Crete did not take the rights of the Sultan into consideration’, and when these events were relayed back to Istanbul, the matter was discussed by the Divan-ı Humayun, the executive council of the Empire, with Çelebi recording the outcome:

Given that the Ottomans were able to assemble in less than six months an invasion fleet in excess of 400 galleys, together with transports and 50,000 troops, it seems highly likely that plans were already in place to undertake the island's conquest. In this respect, the claimed outrage to the Sultan's dignity was little more than subterfuge.

The war over Crete was to last a total of twenty-four years (1645–69); for although Chania fell within two months, Rethymnon the following year, and much of the rest of the island quickly taken, Heraklion was to hold out for twenty years.