Abstract We address an ensemble clustering problem, where reliable clusters are locally embedded in given multiple partitions. We propose a new nonnegative matrix factorization (NMF)-based method, in which locally reliable clusters are explicitly considered by using instance-wise weights over clusters. Our method factorizes the input cluster assignment matrix into two matrices H and W , which are optimized by iteratively 1) updating H and W while keeping the weight matrix constant and 2) updating the weight matrix while keeping H and W constant, alternatively. The weights in the second step were updated by solving a convex problem, which makes our algorithm significantly faster than existing NMF-based ensemble clustering methods. We empirically proved that our method outperformed a lot of cutting-edge ensemble clustering methods by using a variety of datasets.