I built netcdf with mpif90using this option
and compiled the application using mpif90 comipler option.
If your mpif90 is properly built and set up with the same Fortran compiler you are using, it appears that either you didn't build the netcdf Fortran 90 modules with that compiler, or you didn't set the include path for the netcdf modules. This would work the same with mpif90 as with the underlying Fortran compiler.
Syed Ahsan Ali Bokhari
Electronic Engineer (EE)
Research & Development Division
Pakistan Meteorological Department H-8/4, Islamabad.
Phone # off +92518358714
Cell # +923155145014