It is known that Fourier integral operators arising when solving Schrö-dinger-type operators are bounded on the modulation spaces M p,q , for 1 ≤ p = q ≤ ∞, provided their symbols belong to the Sjöstrand class M ∞,1 . However, they generally fail to be bounded on M p,q for p = q. In this paper we study several additional conditions, to be imposed on the phase or on the symbol, which guarantee the boundedness on M p,q for p = q, and between M p,q → M q,p , 1 ≤ q < p ≤ ∞. We also study similar problems for operators acting on Wiener amalgam spaces, recapturing, in particular, some recent results for metaplectic operators. Our arguments make heavily use of the uncertainty principle.