As far as I remember, the vendor has power estimation tools that can help you with that.
Assuming proper data input to the these tools - the estimation accuracy can be quite decent (~25% is what I got) for design purposes.
Another (more accurate and hands on) alternative, will be to acquire an evaluation board with the FPGA you intend to use, connect an A meter in series to the nets in question and take measurements with a functioning design. I had to do it once for a project with very stiff constraints on FPGA current consumption (below 50uA). Didn't trust the estimation tool for such low values...