Standard inference and training with transformer based architectures scale quadratically with input sequence length. This is prohibitively large for a variety of applications especially in web-page translation, query-answering etc. Consequently, several approaches have been developed recently to speedup attention computation by enforcing different attention structures such as sparsity, low-rank, approximating attention using kernels. In this work, we view attention computation as that of nearest neighbor retrieval, and use decision tree based hierarchical navigation to reduce the retrieval cost per query token from linear in sequence length to nearly logarithmic. Based on such hierarchical navigation, we design Treeformer which can use one of two efficient attention layers -- TF-Attention and TC-Attention. TF-Attention computes the attention in a fine-grained style, while TC-Attention is a coarse attention layer which also ensures that the gradients are "dense". To optimize such challenging discrete layers, we propose a two-level bootstrapped training method. Using extensive experiments on standard NLP benchmarks, especially for long-sequences, we demonstrate that our Treeformer architecture can be almost as accurate as baseline Transformer while using 30x lesser FLOPs in the attention layer. Compared to Linformer, the accuracy can be as much as 12% higher while using similar FLOPs in the attention layer.