When granted by Emperor Charles V the island of Malta, the Knights of St. John simply went to use there those flags before used in Rhodes island. Besides, when the Order's Grand Master was aboard on a given ship, this flew a particular ensign quartering the Cross of St. John with the heraldic arms of Grand Master himself.
Source: Adrian Strickland, «The Vexillological Heritage of the Knights of Saint John in Malta», XVII International Congress of Vexillology papers, 1999
Sizes: ensign W12 x L18 mm, mast flags W8 x L12 mm, jack W6 x L9 mm, pennant W4 x L48 mm.