I believe this is open, even if you assume $\mathsf{FP} \neq \mathsf{\# P}$.
It's closely related to parsimonious reductions. If $R,S$ are relations defining languages in NP (that is, $L_R = \{x : (\exists w)[|w| \leq poly(|x|), (x, w) \in R\}$ is in NP). Let $\# R(x) = \#\{w : (x,w) \in R \text{ and } |w| \leq poly(|x|)\}$, the number of witnesses that $x \in L_R$. A poly-time parsimonious reduction is then a many-one reduction $f$ - $x \in L_R$ iff $f(x) \in L_S$ - that furthermore satisfies $\# R(x) = \# S(f(x))$.
Let's call a reduction "weakly parsimonious" (I've seen the concept somewhere before, but don't remember if this is the right name and can't find a reference) if it is like a parsimonious reduction, except that there is additionally a poly-time function $h_2$ (named to be consistent w/ the OQ) such that $\#R(x) = h_2(\#S(f(x)), x)$. If an NP-complete relation/problem is complete under weakly parsimonious reductions, then its associated counting function is $\# P$-complete under many-one reductions.
But the analogous question for many-one versus Turing reductions to define $\mathsf{NP}$-completeness is open, but they are different assuming $\mathsf{NP}$ does not have p-measure zero within $\mathsf{E}$ (Lutz-Mayordomo, see this answer). It would be interesting to see a resolution of this question under a similar resource-bounded measure assumption.