On Pepys' recommendation, the Navy Board reopened the derelict Harwich Dockyard in October 1664 and appointed Deane as its master shipwright, elevating him from being Pett's assistant to his nominal equal.
For Deane, the promotion meant that he would have a free hand in designing and constructing naval vessels, albeit at a smaller dockyard than the great Navy establishments of Portsmouth, Plymouth or Deptford.
One of the first indications of the application to scientific principles to ship construction is found in Pepys' diary, which records that in 1666 "Mr. Deane .
His patron Pepys strongly disapproved of this innovation and the matter was ultimately referred to the King, Charles II, who endorsed Deane's actions.
No longer responsible for shipbuilding at Portsmouth, he still was able to build several ships as a private contractor, mainly at Harwich but also at Rotherhithe.
They were returned for the 1679 Parliament despite both being accused of leaking naval intelligence to France, and being on 9 July 1679 brought before the King's Bench at Westminster on a charge of treason and imprisoned in the Tower of London, but bailed to appear for trial at a later date.