On the supergravity side, we study the propagation of the RR scalar and the dilaton in the D3-branes with NS $B$-field. To obtain the noncommutative effect, we consider the case of $B\to \infty(\theta \to\pi/2)$. We approximate this as the smeared D1-brane background with $F_5=H=0$. In this background, the RR scalar induces an instability of the near-horizon geometry. However, it turns out that the RR scalar is nonpropagating, while the dilaton is a physically propagating mode. We calculate the s-wave absorption cross section of the dilaton. One finds $\sigma_0^\phi |_{B\to\infty} \sim (\tilde \omega \tilde R_{\pi \over 2})^{8.9} / \omega^5$ in the leading-order while $\sigma_0^\phi|_{B=0} \sim (\tilde \omega R_0)^{8}/\omega^5$ in the D3-branes without $B$-field. This means that although the dilaton belongs to a minimally coupled scalar in the absence of $B$-field, it becomes a sort of fixed scalar in the limit of $B \to \infty$.