We propose a scalable way to construct a 3D cluster state for fault-tolerant topological one-way computation (TOWC) even if the entangling two-qubit gates succeed with a small probability. It is shown that fault-tolerant TOWC can be performed with the success probability of the two-qubit gate such as 0.5 (0.1) provided that the unheralded error probability of the two-qubit gate is less than 0.040% (0.016%). Furthermore, the resource usage is considerably suppressed compared to the conventional fault-tolerant schemes with probabilistic two-qubit gates.