Cross-encoder (CE) models which compute similarity by jointly encoding a query-item pair perform better than using dot-product with embedding-based models (dual-encoders) at estimating query-item relevance. Existing approaches perform k-NN search with cross-encoders by approximating the CE similarity with a vector embedding space fit either with dual-encoders (DE) or CUR matrix factorization. DE-based retrieve-and-rerank approaches suffer from poor recall as DE generalizes poorly to new domains and the test-time retrieval with DE is decoupled from the CE. While CUR-based approaches can be more accurate than the DE-based retrieve-and-rerank approach, such approaches require a prohibitively large number of CE calls to compute item embeddings, thus making it impractical for deployment at scale. In this paper, we address these shortcomings with our proposed sparse-matrix factorization based method that efficiently computes latent query and item representations to approximate CE scores and performs k-NN search with the approximate CE similarity. In an offline indexing stage, we compute item embeddings by factorizing a sparse matrix containing query-item CE scores for a set of train queries. Our method produces a high-quality approximation while requiring only a fraction of CE similarity calls as compared to CUR-based methods, and allows for leveraging DE models to initialize the embedding space while avoiding compute- and resource-intensive finetuning of DE via distillation. At test time, we keep item embeddings fixed and perform retrieval over multiple rounds, alternating between a) estimating the test query embedding by minimizing error in approximating CE scores of items retrieved thus far, and b) using the updated test query embedding for retrieving more items in the next round. Our proposed k-NN search method can achieve up to 5 and 54 improvement in k-NN recall for k=1 and 100 respectively over the widely-used DE-based retrieve-and-rerank approach. Furthermore, our proposed approach to index the items by aligning item embeddings with the CE achieves up to 100x and 5x speedup over CUR-based and dual-encoder distillation based approaches respectively while matching or improving k-NN search recall over baselines.