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Traffic matrix (TM) estimation has been extensively studied for decades. Although conventional estimation techniques assume that traffic volumes are unchanged between origins and destinations, packets are often discarded on a path due to traffic burstiness, silent failures, etc. This paper proposes a novel TM estimation method that works correctly even under packet drops. The method is established on a Boolean fault localization technique; the technique requires fewer counters though it only determines whether each link is healthy. This paper extends the Boolean technique so as to deal with traffic volumes with error bounds just by a small number of counters. Along with submodular optimization for the minimum counter placement, we evaluate our method with real network datasets.