The increased performance of mobile terminals has made it feasible to collect data using users' terminals. By making the best use of the network performance data widely collected in this way, network operators should deeply understand the current network conditions, identify the performance-degraded components in the network, and estimate the degree of their performance degradation. For their demands, one powerful solution with such end-to-end data measured by users' terminals is network tomography. Meanwhile, with the advance of network virtualization by software-defined networking, routing is dynamically changed due to congestion or other factors, and each end-to-end measurement flow collected from users may pass through different paths between even the same origin-destination node pair. Therefore, it is difficult and costly to identify through which path each measurement flow has passed, so it is also difficult to naively apply conventional network tomography to such networks where the measurement paths cannot be uniquely determined. We propose a novel network tomography for the networks with undeterministic routing where the measurement flows pass through multiple paths in spite of the origin-destination node pair being the same. The basic idea of our method is to introduce routing probability in accordance with the aggregated information of measurement flows. We present two algorithms and evaluate their performances by comparing them with algorithms of conventional tomography using determined routing information. Moreover, we verify that the proposed algorithms are applicable to a more practical network.