The Council of State was set up by Parliamentary ordinance on 13 February 1649 as a successor to the Derby House Committee which had taken over much of the Privy Council's executive role in the State. It was annually renewed by Parliament and insisted on choosing its own President. From May 1649 it was housed at Whitehall. Membership was reduced from 41 to 15 in 1653 when it became the Protector's Council. By 1656 it was being styled the Privy Council. After Richard Cromwell's abdication in 1659 the Council of State was revived and remodelled twice before it relapsed into a Privy Council. It spawned committees, both standing and ad hoc; the former were the Admiralty, the Ordnance, the Mint Committee, the Irish, the Private Examinations and the Foreign Negotiations Committees.
The Commissioners of the Navy or Navy Commissioners, who replaced the principal royal officers on 15 September 1642, when 12 were appointed, had an administrative role. They kept the fleet afloat, and took their instructions from the Admiralty. They sat in Mincing Lane until 1649, at the Victualling Office on Tower Hill 1649-1653, and subsequently in Seething Lane in what became the Navy Office for some time, with additional recruits. This was a period of phenomenal naval expansion, first to meet the royalist threat from Prince Rupert's fleet, then from the Dutch, which led to the first Dutch War, and finally to promote an aggressive policy towards Spain in the Mediterranean and the Caribbean, creating two long term naval stations. In wartime the Commissioners took up residence in the naval dockyards.
On 12 March 1649 the council set up its standing Admiralty committee (of just three, then, but subsequently added to) to oversee daily and to advise it, but retained the powers of Admiralty. In December 1652, when the first Dutch War was going badly for the fleet, Parliament created eight Commissioners of Admiralty and the Navy. Under Oliver's Protectorate, their presiding genius Sir Henry Vane was displaced, and eleven commissioners wielded the Admiralty powers from 1653. The restored Rump merely changed their composition in 1659, but the restored monarchy disposed of them.
The Parliamentary Navy Committee, first appointed 25 August 1641, exercised financial control over expenditure on the navy. After 1645 it took on the Customs as well. Although after the King's execution this committee seemed set to have its role expanded, it was soon eclipsed by the Admiralty Committee of the Council of State, which was more expert. The committee was dispensed with by Oliver Cromwell on 20 April 1653.