Acoustic intensity is usually estimated by the cross-spectrum of acoustic pressure at two adjacent microphones. The cross-spectrum calculated by digital Fourier transform technique will unavoidably have leakage error since the period of signal will not be usually coincident with record length. Therefore, the acoustic intensity estimated by the conventional FFT analyzer will show distorted value. In this paper, the expression of the Fourier transformed data of a harmonic signal with a single frequency is formulated when there is leakage error. The method to eliminate the effect of leakage error from the contaminated data is also proposed. Some numerical examples show the validation of the proposed method.