Recently network bandwidth becomes a performance concern particularly for collective communication since bisection bandwidths of supercomputers become far less than their full bisection bandwidths. In this context we propose the use of a network coding technique to reduce the number of unicasts and the size of data transferred in latency-sensitive collective communications in supercomputers. Our proposed network coding scheme has a hierarchical multicasting structure with intra-group and inter-group unicasts. Quantitative analysis show that the aggregate path hop counts by our hierarchical network coding decrease as much as 94% when compared to conventional unicast-based multicasts. We validate these results by cycle-accurate network simulations. In 1,024-switch networks, the network reduces the execution time of collective communications as much as 70%. We also show that our hierarchical network coding is beneficial for any packet size.