Let $Sc(vL)$ be the cyclotomic $q$-Schur algebra associated to the Ariki-Koike algebra $He_{n,r}$, introduced by Dipper-James-Mathas. In this paper, we consider $v$-decomposition numbers of $Sc(vL)$, namely decomposition numbers with respect to the Jantzen filtrations of Weyl modules. We prove, as a $v$-analogue of the result obtained by Shoji-Wada, a product formula for $v$-decomposition numbers of $Sc(vL)$, which asserts that certain $v$-decomposition numbers are expressed as a product of $v$-decomposition numbers for various cyclotomic $q$-Schur algebras associated to Ariki-koike algebras $He_{n_i,r_i}$ of smaller rank. Moreover we prove a similar formula for $v$-decomposition numbers of $He_{n,r}$ by using a Schur functor.