In 1613 Whitelocke's opposition to the prerogative brought him into sharp collision with the crown. The administration of the navy stood in urgent need of reform, and in the winter of 1612–13 a preliminary step was taken by the issue of a commission investing the lord high admiral (Charles Howard, 1st Earl of Nottingham), Lord Chancellor Ellesmere, the lord privy seal and lord chamberlain with extraordinary powers for the investigation of abuses and the trial of offenders. As legal adviser to Sir Robert Mansell, who was interested in defeating the investigation, Whitelocke drew up a series of 'exceptions' to the commission, in which he very strictly circumscribed the prerogative. A copy of the exceptions came into the hands of the crown lawyers, who at once suspected that they were Whitelocke's. Evidence was wanting; but his contemporaneous opposition to the transfer of a cause in which he was retained from the chancery to the court of the Earl Marshal furnished a pretext for his committal to Fleet Prison (18 May); and he was not released until he had made full submission in writing (13 June).