The Bogomolov conjecture claims that a closed subvariety containing a dense subset of small points is a special kind of subvariety. In the arithmetic setting over number fields, the Bogomolov conjecture for abelian varieties has already been established as a theorem of Ullmo and Zhang, but in the geometric setting over function fields, it has not yet been solved completely. There are only some partial results known such as the totally degenerate case due to Gubler and our recent work generalizing Gubler’s result. The key in establishing the previous results on the Bogomolov conjecture is the equidistribution method due to Szpiro, Ullmo and Zhang with respect to the canonical measures. In this paper we exhibit the limits of this method, making an important contribution to the geometric version of the conjecture. In fact, by the crucial investigation of the support of the canonical measure on a subvariety, we show that the conjecture in full generality holds if the conjecture holds for abelian varieties which have anywhere good reduction. As a consequence, we establish a partial answer that generalizes our previous result.