Se file.csv
for assim:
123456789,123456789,123456789,123456789,123456789
123456789,123456789,123456789,123456789,223456789
123456789,123456789,123456789,123456789,323456789
123456789,123456789,123456789,123456789,423456789
Então, você pode fazer:
$ awk -F, '{print $1","$2","$3","$4","substr($5,1,5) }' file.csv
123456789,123456789,123456789,123456789,12345
123456789,123456789,123456789,123456789,22345
123456789,123456789,123456789,123456789,32345
123456789,123456789,123456789,123456789,42345