Based on the work of Chen, Lü, and Pope, we derive expressions for the D≥6 dimensional metric for Kerr-anti-de Sitter black holes with two independent rotation parameters and all others set equal to zero: a1≠0, a2≠0, a3=a4=⋯=0. The Klein-Gordon equation is then explicitly separated on this background. For D≥6 this separation results in a radial equation coupled to two generalized spheroidal angular equations. We then develop a full numerical approach that utilizes the asymptotic iteration method to find radial quasinormal modes of doubly rotating flat Myers-Perry black holes for slow rotations. We also develop perturbative expansions for the angular quantum numbers in powers of the rotation parameters up to second order.