In 1578 Perrot was accused by his deputy-Admiral, Richard Vaughan, of tyranny, subversion of justice, and dealing with pirates. The accusations may have been exaggerated, and Perrot retained the confidence of the Crown: in the same year he was appointed commissioner for piracy in Pembrokeshire, and in the following year was given command of a naval squadron charged with the interception of Spanish ships on the Irish coast. In 1579, during a voyage to Ireland, he chased a pirate ship to the Flemish coast and captured the commander, Deryfold. On her approach to the Thames estuary Perrot's ship was struck by a storm, and while all on board prepared for death Perrot said to his son, Thomas, "Well Boy, God bless you and I give you my blessing. I wish to God that you were ashore and the Queen's ship safe then I should care the less about myself". The ship was saved with the skill of the captive Deryfold, who was pardoned by the Queen on Perrot's petition.