Ms Percy, who was chief executive for nine years, said she "firmly believed" it was her responsibility to stay on to "oversee improvements" and was taking on a new role with Southern Health providing "strategic advice to local GP leaders".
She said she understood why "many will say I should have stepped down sooner given the very public concerns which have been raised in the past months".
A spokeswoman for the trust said Ms Percy's salary - which is quoted in the trust's annual report as between £180,000 and £190,000 - will remain the same when she moves to the advisory role.
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