If you need the protein sequence then you can iterate over your list of accession numbers and create links in the format of the link above. The "all" genomes directory is large and it may timeout in a browser. You will have to map your accession numbers to GCF* numbers.

A possible loop can be as simple as

#!/bin/bash

for i in `cat your_accession_number_file.txt`;

do wget ftp://ftp.ncbi.nlm.nih.gov/genomes/all/$i/$i\_protein.faa.gz

done;