This paper studies real-time deterministic prediction of wave-induced ship motions using the autocorrelation functions (ACFs) from short-time measurements, namely the instantaneous ACFs. The Prolate Spheroidal Wave Functions (PSWF) are introduced to correct the large lag time errors in the instantaneous sample ACF, together with a modification of the autocorrelation (AC) matrix for ensuring its positive definiteness. The validity of the PSWF-based ACFs is first examined by using the ship motion measurements from model experiment under stationary wave excitations. It is shown that the use of PSWFbased ACFs leads to better prediction accuracy than direct use of sample ACFs. The validation is then extended to ship motion prediction using in-service data from a container ship, and an improvement of the prediction accuracy by PSWF-based ACFs is again found. Finally, the effectiveness of use of the instantaneous ACFs for non-stationary wave-induced responses is highlighted by comparing with the prediction results based on the ACFs from long-time measurements.