I've had this problem as well. It's generally not 'water' freezing in the intake pipe, it's due more to the fact your intake and exhaust ducts ate too close together, the exhaust releases warm exhaust with condensate (warm moist gases), which are drawn to the nearby intake. The problem is exacerbated if your intake vent/pipe has a mesh screen, (wire or pvc
mesh) used to keep debris or critters out of the pipe. The mesh creates more surface area, increases cooling and frost build up. Other internet experts recommend adding 90 degree bends or extensions to the pipe, but they don't say that each bend or extention increases distance, and resistance to airflow which can overwork your draft inducer, shortening it's life and decreasing efficiency.
I solved my problem by installing a 2 inch to 4 inch pvc pipe transition, I used 1/2 inch chicken wire as a critter shield, then painted it flat black. The system works, the flat black paint absorbs solar radiation adding just enough heat to stop frosting over. It was -30 degrees last winter and it never frosted over.