Apart from being annoying, this condition can allow the toilet to leak or, under certain conditions, to crack.
Shims are one way of dealing with the problem.
Don't use wood shims. Wood and water don't mix. Plastic shims are available specifically for this purpose. Put the toilet into place and make a pencil mark on the floor around the base of the toilet. Shim it up using plastic shims that are generally available in the plumbing section of your hardware store.