Perhaps the most prevalent public image of the Royal Navy of the French Wars is of the shipboard flogging of sailors. Naval discipline and in particular the practice of flogging is subject to much historical controversy. Views on the subject of flogging range from the use of the lash as a brutal and brutalising imposition of authority over oppressed and impressed sailors to flogging as a minor imposition on men who would prefer to receive instant retribution for their offences rather than suffer trial and incarceration at some future date.

Works by J. D. Byrn Jr, Crime and Punishment in the Royal Navy and Naval Court Martials 1793–1815, look at Royal Navy discipline in the social context of the times, as well as applying a systematic approach to the subject. Byrn's thesis is that naval discipline conformed in most respects to how law and order was conducted on land in contemporary society:

In his analysis Byrn examined all the extant court-martial records for the period and station in question, as well as other contemporary naval records including ship's muster books. This chapter attempts to take Byrn's work forward by concentrating on how discipline was used to manage a ship's company on a day-to-day basis.