Goussarov, Polyak and Viro defined a finite type invariant and a local move called an n-variation for virtual knots. In this paper, we give the differences of the values of the finite type invariants of degree 2 and 3 between two virtual knots which can be transformed into each other by a 2- and 3-variation, respectively. As a result, we obtain lower bounds of the distance between long virtual knots by 2-variations and the distance between virtual knots by 3-variations by using the values of the finite type invariants of degree 2 and 3, respectively. © 2013 World Scientific Publishing Company.