Hood is set to join Brunswick early next month as chief of office, working closely with Brunswick founder and senior partner Alan Parker.
It is believed Hood will handle much of the agency's management, leaving Parker to concentrate on agency clients and strategy.
Industry sources claim Hood's move may raise conflict of interest issues as Brunswick clients include Rolls-Royce and Smiths Industries, which both supply to the defence sector indirectly.
However, an agency spokesman said the agency had no direct defence clients and that Hood's role would not involve client-facing work.
'There is no question or even the slightest possibility of any conflict of interest,' said the spokesman.
Hood's replacement has not yet been appointed at the MoD, but recruitment is set to be carried out during the summer.
Prior to his role as Hoon's special adviser, Hood acted as senior political adviser to the then foreign secretary Robin Cook. He also launched Policy Network in 2000 to bring together policy units and policy advisers from around the world.
Meanwhile, the MoD has announced that it has recruited Sunday Times defence correspondent James Clark. It is understood he will take on a media relations management role within the corporate communications team.