As a Loyalist Protestant who spoke both Irish and English, he was tasked with suppressing potential rebellion in the county amid rumors of a French invasion.
A teacher of French named Wright in the town of Clonmel was flogged and mistreated so badly that he later won a judgement of five hundred pounds against Judkin-Fitzgerald.
After hearings before a secret committee, Parliament passed a special indemnity act to protect Judkin-Fitzgerald, but not without considerable debate and criticism.
The bitterness of Irish Republicans towards Judkin-Fitzgerald can be seen in the obituary published in The Irish Magazine, October 1810, which said in part, "The history of his life and his loyalty is written in legible characters on the backs of his countrymen, his enormities were so various, and the fertility of his imagination in devising new modes of desolation and torture were so truly original that expresses and relays of horses were every day employed to give the earliest intelligence of their effect through the country, for the instruction of other gentlemen, who had the management of Whipping Districts.
John Judkin-Fitzgerald (1787-1860) succeeded to the baronetcy; he also served as High Sheriff of Tipperary (in 1819) and as mayor of Cashel; he died in the wreck of the PS Nimrod.