Seems some issue with my environment. After fix this env issue I was able to build octave with fft support using following configuration settings.
./configure --prefix=/tmp/octa12 CFLAGS=-fPIC CXXFLAGS=-fPIC --enable-shared --with-qt --with-blas=/octave/v5.1.0/BLAS-3.8.0/blas_LINUX.a --with-lapack=/octave/v5.1.0/lapack-3.8.0/liblapack.a --with-fftw3-includedir=/home/niraj/fftw/include/ --with-fftw3-libdir=/home/niraj/fftw/lib --with-fftw3f-includedir=/home/niraj/fftw/include --with-fftw3f-libdir=/home/niraj/fftw/lib
Thanks for your support.
Thanks
Niraj