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We consider the problem of accurate channel estimation for OTFS based systems with few transmit/receive antennas, where additional sparsity due to large number of antennas is not a possibility. For such systems the sparsity of the effective delay-Doppler (DD) domain channel is adversely affected in the presence of channel path delay and Doppler shifts which are non-integer multiples of the delay and Doppler domain resolution. The sparsity is also adversely affected when practical transmit and receive pulses are used. In this paper we propose a Modified Maximum Likelihood Channel Estimation (M-MLE) method for OTFS based systems which exploits the fine delay and Doppler domain resolution of the OTFS modulated signal to decouple the joint estimation of the channel parameters (i.e., channel gain, delay and Doppler shift) of all channel paths into separate estimation of the channel parameters for each path. We further observe that with fine delay and Doppler domain resolution, the received DD domain signal along a particular channel path can be written as a product of a delay domain term and a Doppler domain term where the delay domain term is primarily dependent on the delay of this path and the Doppler domain term is primarily dependent on the Doppler shift of this path. This allows us to propose another method termed as the two-step method (TSE), where the joint two-dimensional estimation of the delay and Doppler shift of a particular path in the M-MLE method is further decoupled into two separate one-dimensional estimation for the delay and for the Doppler shift of that path. Simulations reveal that the proposed methods (M-MLE and TSE) achieve better channel estimation accuracy at lower complexity when compared to other known methods for accurate OTFS channel estimation.