Barker was beaten by the Larry Ellison-backed holders Team Oracle USA, who produced a stunning comeback from 8-1 down to retain the Cup 9-8 on San Francisco Bay in 2013.
"This is an incredible opportunity to build a new team from the ground up," Barker told the America's Cup organisers website after he confirmed the new role in Bermuda, which will host the 35th America's Cup regatta in 2017.
"It's an honour to take on the responsibility of both CEO and skipper of ...Team Japan.
"We're filling the key roles on the team as quickly as we can. I think were pulling together a very strong team.
"We want to compete at the head of the fleet and were assembling a team that is capable of doing that.
"Our goal is to win the America's Cup."
Japan was confirmed as a challenger for the next regatta last month after Italian syndicate Luna Rossa withdrew in protest at the organisers' decision to change the size of the yacht to be used.
Oracle and the challenging syndicates from Sweden, France, Britain, Italy and New Zealand had initially agreed on a 62-foot foiling catamaran, known as an AC62, for the next event.
However, Oracle and the Swedish, French and British challengers then opted to reduce the size of the boat to an AC45 class, which drew protests from the New Zealanders and Italians who had already begun development work on the bigger yacht.
TNZ, whose own challenge had been in doubt after organisers withdrew the offer to hold a warm-up regatta in Auckland prior to the America's Cup in Bermuda, have had better news in recent weeks with the confirmation of key sponsorship agreements.
Airline Emirates and watchmaker Omega confirmed they would support the team after the New Zealand government all but withdrew any potential financial support after the Auckland regatta was cancelled.
TNZ have appealed the organisers' decision to cancel the Auckland event.
(Reporting by Greg Stutchbury in Wellington; Editing by Peter Rutherford)
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