In this letter, we introduce an efficient algorithm to estimate the noise correlation matrix in the initial stage of the hyperspectral signal identification by minimum error (H<sc>y</sc>S<sc>ime</sc>) method, commonly used for signal subspace identification in remotely sensed hyperspectral images. Compared with the current implementations of this stage, the new algorithm for noise estimation relies on the reliable QR factorization, producing correct results even when operating with single-precision arithmetic. Additionally, our algorithm exhibits a lower computational cost, and it is highly parallel. The experiments on a multicore server, using two real hyperspectral scenes, expose that these theoretical advantages carry over to the practical results.