The ambiguity in dependency analysis of Japanese predicates has been one of the major causes of the failure of long sentence analyses. To overcome this problem, a new dependency analysis method for Japanese subordinate clauses based on semantically embedded structures was proposed and its accuracy was evaluated. In this paper, the three levels of hierarchical subordinate clauses proposed by the Japanese philologist Minami, were reviewed for their syntax and semantics, and broken down into 13 basic categories and 4 detailed categories. A hierarchical ordering of these categories yields the dependency relations between predicates. Experiments were conducted with some 972 newspaper article sentences (totaling 2,327 predicates of which 661 are classified as having ambiguous dependency). Whereas the conventional method leaves 356 predicates of ambiguous dependency, this number was reduced to 54 predicates by the new method Accordingly, the accuracy of the first candidate of the dependency relations within a sentence was improved from 92% to 98%.