The way I've done it is to create three vectors, all the same length. x1 to xn, y1 to yn and z1 to zn.
The at point (x1,y1) z1 is the variable I wish to produce a contour map.This is how I've defined the grid of points.
There are probably better ways to do it but my data is already in this format and the contour plot appears as I would expect it to.