Ferm's robust Presbyterianism got him into trouble on the reconstitution of episcopacy. In October 1600
Peter Blackburn was appointed bishop of Aberdeen, with a seat in parliament. Ferm denounced this innovation. In February 1605 he appeared before the
Privy Council with
John Forbes, to justify their excommunication of the
Earl of Huntly. He was a delegate to the General Assembly which met at Aberdeen on 2 July, and was about to hold proceedings, contrary to
the king's injunction. For this irregularity, Ferm and around 20 others were arrested and interrogated; some apologised and were released, but thirteen were imprisoned in various castles across Scotland; on 3 October Ferme was confined to
Doune Castle, Perthshire, at his own expenses. Confined with him in Doune was another attendee at the Aberdeen general assembly,
John Munro of Tain. On 24 October he was summoned to appear before the privy council, but would not own its authority in causes spiritual, and, along with Munro, made his escape. He was again cited for 24 February 1607, appeared before the council on 20 May, and again escaped, hiding himself for four days in Edinburgh. Although Ferm had been condemned to a period of banishment on the
island of Bute, it is by no means certain that he was ever there. His first escape, from the castle of Doune, took place at a time when he was being transferred from Doune into the custody of depute-sheriffs who were due to deliver him to Bute; and after the second escape, from Edinburgh, there is no mention in the records of recapture or imprisonment . A contemporary,
John Forbes, suggests that Ferm had indeed been imprisoned on Bute for three years; but Forbes himself had been exiled to France in 1606, and was in no position to know what had happened to his colleagues in Scotland. The minutes of the Presbytery of Deer, to which the Fraserburgh church reported, indicate that Ferm was never absent from Fraserburgh for more than three months between 1607 and 1610. ==Later life==