The detection of sinusoidal signals embedded in noise is an important topic in passive sonar signal processing. The performance of existing tone detection techniques is limited by the Doppler frequency shift, which is caused by the relative motion between moving targets and the receiver. In this study, an algorithm based on long-time coherent integration is proposed to achieve robust tonal signal detection under the influence of a Doppler frequency shift. First, the received narrowband signals radiated by moving targets are split into multiple segments through a window-length constraint. The results obtained by applying a discrete Fourier transform (DFT) to the data segments are modeled as a polynomial phase signal in the frequency domain. Then, the polynomial Radon-polynomial Fourier transform (PRPFT) is applied to simultaneously compensate the time-variant frequency drift and phase difference. To avoid the gain loss due to the discretization of the phase difference compensation in PRPFT, a phase compensation factor searching algorithm is proposed. The simulation results show that the proposed algorithm can provide higher frequency resolution and higher coherent integration gain even in the case of a severe Doppler shift. Furthermore, the results of sea trials demonstrate that the proposed method can perfectly achieve coherent integration for signals with a duration of several hundred seconds under different experimental conditions.