In this paper, we study and propose an inter-cell co-channel interference (CCI) mitigation method for pilot signals using cyclic shift Zadoff-Chu (CS-ZC) sequences for SC-FDMA-based uplink without tight scheduler coordination among cells. Firstly, we investigate the issue of severe detection performance degradation created by the lack of orthogonality among the pilot signals without alignment of the allocated frequency resource positions among cells when using the conventional CS-ZC sequences generation scheme. Secondly, we identify the primary factor causing the issue. Thirdly, we propose a frequency-dependent CS-ZC sequence generation scheme by allocating the same spectrum elements of the ZC sequence to the overlapped subcarriers among cells to mitigate the inter-cell CCI of the pilot signals without alignment of the frequency resource positions among cells. Finally, we confirm the validity of the proposal using uplink data BLER evaluation under a multipath fading condition by computer simulation compared to the conventional method, and show that the proposal achieves around 0.9 dB and 0.6 dB better performance at 10% BLER than the conventional method for 1 RB and 2 RBs frequency offsets in 3 RBs transmission bandwidth, respectively.