The Partial Element Equivalent Circuit (PEEC) method is promising numerical technique for three-dimension electromagnetic modeling across various application fields. In the framework of the PEEC method, the partial elements modeling the magnetic and electric field coupling between elementary volumes and surfaces are computed by double-folded volume and surface integrals. Assuming the quasi-static hypothesis and an orthogonal mesh, the integrals have been computed by the analytical formulas derived in literature, which significantly reduces the computational time in comparison to the numerical integration. However, the existing analytical formulas are affected by significant numerical errors for certain PEEC structural mesh necessary to model the skin and proximity effects with a higher accuracy. To utilize the full potential of the PEEC method, the calculation of partial elements has to be carefully addressed, which has not been investigated in a comprehensive way so far. Accordingly, this paper presents a systematic accuracy analysis of the existing closed-form analytical formulas and methods for calculating the self and mutual inductances between two rectangular conductors. Additionally, a new strategy to select a proper analytical formula depending on the dimensions and positions of two conductors is proposed, which allows the mutual inductance extraction with a relative error of less than 0.1 % . The new method is systematically validated on examples of 3-D dense PEEC systems using the quadruple precision arithmetic as reference.