Experimental study of low-frequency dynamics of an intracavity frequency-doubled Nd:YAG laser demonstrates the influence of the interaction of orthogonally polarized modes, participating in frequency doubling (type II phase matching), on the stability of the laser output. At a sufficiently low pump rate and low conversion efficiency, the laser shows stable operation with a low noise level at the frequencies of relaxation oscillations. At a high pump power and/or a high conversion efficiency, the laser emission becomes unstable as a result of Hopf bifurcation at the frequencies of relaxation oscillations that are responsible for the anti-phase polarization dynamics of the laser.