The two-channel Generalized Sidelobe Canceller (GSC) scheme suffers from the presence of leakage signal in the reference channel. The leakage signal is caused by the dissimilar impulse responses between microphones, and different paths from speech source to microphones. Such leakage is detrimental to speech enhancement of the GSC since the desired reference signal becomes corrupted. In order to suppress the signal leakage, two matrix injection methods are proposed. In the first method, a simple gain compensation matrix is used. In the second, a projection matrix for reducing the error between the actual and the ideal primary and reference signals, is used. This paper describes the performance degradation resulting from leakage, and proposes effective methods to resolve the problem. Representative experiments were conducted to demonstrate the effectiveness of the proposed methods on recorded speech and noise in an actual automobile environment.