The shortcomings of paymaster accountability measures and the flaws in the crown's implementation of them created a vacuum in which the trésoriers were able to advance their personal interests at the expense of the navy. Assessing the scale of misappropriation that occurred in the naval treasury under Louis XIV is a difficult task since most of the trésoriers’ improper activities escaped the crown's immediate attention and ministers privileged the effective execution of the war effort over potentially costly meddling in the trésoriers’ financial affairs. Nonetheless, there were suggestions of misconduct by the paymasters as the naval administration went through its various accounts: the trésoriers were cautioned for moving funds without the naval minister's consent; there was suspicion that the lack of receipts from the trésoriers’ commis was not always caused by the naval intendants and ordonnateurs failing to provide them on time; and the routine complications that administrators encountered in ascertaining the navy's extraordinary income in the ports suggest that the trésoriers, who acted as primary revenue receivers in this regard, misspent the funds.

The navy's trésoriers were typically punished for misappropriating funds only when the crown was not preoccupied with the overriding demands of meeting wartime expenditure. The periodic fiscal enquiries were initiated by the crown to punish financiers for misconduct and fraudulent activity, although some of the most important individuals who had bankrolled the crown in war escaped scrutiny, and the proceedings could be used by its instigators as a means of displacing established financial arrangements with their own client networks, as Jean-Baptiste Colbert successfully achieved through the Chambre de justice of 1661–65. During the Chambre de justice that was opened in 1661, and which investigated fiscal wrongdoing in the period between 1635 and 1661, the financial affairs of the navy's trésoriers were scrutinised, alongside those of other major comptables and traitants. In particular, Claude and Georges Pellissary, the brothers who dominated the naval treasury between 1648 and 1676, faced a total tax charge of 220,000 l., although this was later reduced by 100,000 l. Equally, following Louis XIV's reign, the Chambre de justice of 1716–17 imposed substantial financial penalties reaching almost 2.7 million l. on the naval and galley fleet trésoriers that it investigated, although only 1.5 million l. was ultimately recovered after several reductions in fines were granted.