Using the HAL QCD method, we investigate S-wave meson-baryon interactions in singlet and two octet channels in the flavor SU(3) limit, where the chiral unitary model predicts that a combination of bound-state poles in these channels corresponds to $\Lambda(1405)$. To avoid the singular behavior of the leading-order potentials of these channels in the derivative expansion, we instead employ a separable potential in the time-dependent HAL QCD method. To calculate all-to-all propagators in the three-point correlation functions including $\Lambda$-baryon source operators with zero momentum, we employ the conventional stochastic estimation combined with the covariant approximation averaging. Separable potentials both in the singlet and octet channels show attraction without singular behavior. Our results of the corresponding phase shifts indicate that the attractive interaction in the singlet channel is stronger than that in the octet. Binding energies are consistent with the estimates from the two-point correlation function within one (two) sigma for the singlet (octet) channel, and this ordering of binding energies is consistent with the mass hierarchy suggested by the chiral unitary model.