Implantable ventricular assist devices (iVADs) are commonly used to treat patients with severe heart failure. To ensure safe and reliable operation of iVADs, it is crucial to develop a method for estimating the flow rate (Q) of the centrifugal blood pump used in iVAD without relying on a flowmeter. To address this need, we previously developed a flow rate estimation method (FEM-r) that focuses on the correlation between Q and the levitation position (r) of an impeller suspended by a magnetic bearing in a centrifugal blood pump. The FEM-r maintains a high level of estimation accuracy even when changes in blood viscosity are expected during treatment. This advantageous characteristic distinguishes FEM-r from the conventional method (FEM-I_MT) that employs motor current as an estimation index. However, a drawback of FEM-r is the requirement for an additional displacement sensor to measure r. In this study, we propose a solution to this issue by leveraging the correlation between r and the balance of currents (I_EMs) flowing through the electromagnets in a magnetic bearing. Thus, we propose an estimation method called FEM-I_EM, which utilizes the balance of I_EMs as a flow rate estimation index. The balance of I_EMs can be obtained using the minimum number of sensors required for iVAD control. First, we developed an estimation equation for FEM-I_EM and determined its estimation coefficients by multiple regression analysis based on the data obtained from experiments using a mock loop. The root mean square error (RMSE) and determination coefficient (R²) of the multiple regression analysis were 0.293 L/min and 0.965, respectively. The RMSE between the estimated and measured Q values were 0.284, 0.347, and 1.069 L/min for FEM-I_EM, FEM-r, and FEM-I_MT, respectively, indicating that the accuracy of FEM-I_EM was comparable to that of FEM-r and significantly higher than that of FEM-I_MT. Thus, the simple FEM-I_EM proposed in this study demonstrates excellent performance for clinical use, allowing accurate flow rate estimation of a centrifugal blood pump without requiring additional position sensor, viscosity measurement, or compensation method, even when the blood viscosity fluctuates.