This letter focuses on reconfigurable intelligent surface (RIS) assisted multiple-input multiple-output (MIMO) systems, wherein an attacker is free to conduct a controller manipulating attack or electromagnetic interference (EMI) against RIS. We first consider attack detection, then identify the type of attack. When the type is identified as EMI, we investigate countermeasures by estimating and eliminating the received EMI. Finally, the optimization algorithm is proposed to enhance signal-to-interference plus noise ratio with EMI elimination. All the proposed schemes are based on physical-layer symbols without secret keys. The effectiveness of the proposed schemes has been validated by numerical or analytical results.