The following description of the duty of the Clerk of the Acts shows the importance of the office, and the statement that if the clerk is not fitted to act as a commissioner he is a blockhead and unfit for his employment is particularly racy, and not quite the form of expression one would expect to find in an official document: 

“Clerkeof the acts.

“The clarke of the Navye’s duty depends principally upon rateing (by the Board’s approbation) of all bills and recording of them, and all orders, contracts & warrants, making up and casting of accompts, framing and writing answers to letters, orders, and commands from the Councell, Lord High Admirall, or Commissioners of the Admiralty, and he ought to be a very able accomptant, well versed in Navall affairs and all inferior officers dutyes.

“It hath been objected by some that the Clarke of the Acts ought to be subordinate to the rest of the Commissioners, and not to be joyned in equall power with them, although he was so constituted from the first institution, which hath been an opinion only of some to keep him at a distance, least he might be thought too forward if he had joynt power in discovering or argueing against that which peradventure private interest would have concealed; it is certaine no man sees more of the Navye’s Transactions than himselfe, and possibly may speak as much to the project if required, or else he is a blockhead, and not fitt for that imployment.  But why he should not make as able a Commissioner as a Shipp wright lett wise men judge.”

In Pepys’s patent the salary is stated to be L33 6s. 8d., but this was only the ancient “fee out of the Exchequer,” which had been attached to the office for more than a century.  Pepys’s salary had been previously fixed at L350 a-year.

Neither of the two qualifications upon which particular stress is laid in the above Instructions was possessed by Pepys.  He knew nothing about the navy, and so little of accounts that apparently he learned the multiplication table for the first time in July, 1661.  We see from the particulars given in the Diary how hard he worked to obtain the knowledge required in his office, and in consequence of his assiduity he soon became a model official.  When Pepys became Clerk of the Acts he took up his residence at the Navy Office, a large building situated between Crutched Friars and Seething Lane, with an entrance in each of those places.  On July 4th, 1660, he went with Commissioner Pett to view the houses, and was very pleased with them, but he feared that the more influential officers would jockey him out of his rights.  His fears were not well grounded, and on July 18th he records the fact that he dined in his own apartments, which were situated in the Seething Lane front.

On July 24th, 1660, Pepys was sworn in as Lord Sandwich’s deputy for a Clerkship of the Privy Seal.  This office, which he did not think much of at first, brought him “in for a time L3 a day.”  In June, 1660, he was made Master of Arts by proxy, and soon afterwards he was sworn in as a justice of the Peace for Middlesex, Essex, Kent, and Hampshire, the counties in which the chief dockyards were situated.