In this paper, we investigate the frequency domain channel estimation for multiple-input multiple-output (MIMO) single-carrier frequency-division multiple-access (SC-FDMA) systems. In MIMO SC-FDMA, code-division multiplexed (CDM) pilots such as cyclic-shifted Zadoff-Chu sequences have been adopted for channel estimation. However, most frequency domain channel estimation schemes were developed based on frequency-division multiplexing of pilots. We first develop a channel estimation error model by using CDM pilots, and then analyze the mean-square error (MSE) of various minimum MSE (MMSE) frequency domain channel estimation techniques. We show that the cascaded one-dimensional robust MMSE (C1D-RMMSE) technique is complexity-efficient, but it suffers from performance degradation due to the channel correlation mismatch when compared to the two-dimensional MMSE (2D-MMSE) technique. To improve the performance of C1D-RMMSE, we design a robust iterative channel estimation (RITCE) with a frequency replacement (FR) algorithm. After deriving the MSE of iterative channel estimation, we optimize the FR algorithm in terms of the MSE. Then, a low-complexity adaptation method is proposed for practical MIMO SC-FDMA systems, wherein FR is performed according to the reliability of the data estimates. Simulation results show that the proposed RITCE technique effectively improves the performance of C1D-RMMSE, thus providing a better performance-complexity tradeoff than 2D-MMSE.