In theory, the crown had several measures at its disposal to control the flow and distribution of funds. The trésoriers experienced checks on their handling of royal funds at three key points: throughout their exercices via the payment orders written by the naval minister; at the point of disbursement in the dockyards where the intendant, seconded by a contrôleur particulier (auditor or comptroller), was given copies of the payment orders sent to the trésorier's commis and then compiled registers of completed remittances; and finally, at the end of the exercice when the trésorier presented a provisional balance sheet, known as the état au vrai, to the Conseil royal des finances, which then closed his exercice before detailed accounts were sent to the Chambre des comptes to be cleared according to the financial regulations set out in the edict of August 1669. However, in practice, inherent weaknesses and implementation difficulties complicated auditing efforts and limited the crown's ability to enforce its financial controls, thus allowing the trésoriers to operate without any effective accountability.

As Legohérel first examined, the fiscal-financial regulations written into the Ordonnance de la Marine by Colbert and his son, the marquis de Seignelay, were principally concerned with maintaining the separation of ordonnateurs and paymasters. In an administrative and fiscal system where powers were widely devolved to officers and commissioners and the potential for manipulation and misappropriation of funds was significant, it was critical to ensure that royal funds were handled only by the trésoriers from the point of receipt to the point of disbursement, and not by the naval intendants and the commissaires ordonnateurs who ordered and authorised expenditure. While this strict division of responsibility was broadly sustained (despite instances of incompetence or abuse) by virtue of the incentives the trésoriers had to maintain control over the flow of funds, the regulations controlling the activities of the trésoriers were limited and often weakly implemented.

In terms of its ability to hold the trésoriers directly accountable, the naval ministry exercised loose control since it lacked the means to verify that the trésoriers were following its remittance instructions.