Cassar developed an uneasy relationship with the island's governor, Fra Ferdinando de Rosolmini, which led to him being recalled back to Malta in August 1603 after being repeatedly reprimand due to the slow progress of the works.
[4] However, military historian Stephen C. Spiteri states that he died in around mid-June 1609,[5] and some records suggest that he was buried in Valletta.
The only evidence of his work as a military engineer are documents relating to his directing the rebuilding of the Cittadella between 1600 and 1603, and mentions of preliminary sketches of the Garzes Tower dated 1601–02.
As early as 1647, Giovanni Francesco Abela attributed the design of the Saint Mary's Tower on Comino (built 1618) to Cassar.
[3] Between the 1590s and 1606, the Inquisition accused and sentenced Cassar for practicing fortune-telling, and he was said to be able to relieve people and read their future.
It is now believed that Cassar's "sins" included possession of banned manuscripts about magic which he had obtained in Messina.