The command to list the directories using the most inodes is:
find . -printf "%h\n" | cut -d/ -f-2 | sort | uniq -c | sort -rn
However, I first needed to narrow down the directory under root that might be causing the problem:
df -i
showed that the root directory (/) was the problem. But I did not need to scan all directories as some had terabytes of files so:
for DIR in $( ls | egrep -v "local|var|home|mnt|boot|dev" ) ;do find /$DIR -printf "%h\n" | cut -d/ -f-2 | sort | uniq -c | sort -rn ; done
This was much quicker and I quickly narrowed it down to /usr/local/pnp4nagios/spool