Great.
I have updated the payu/1.2.0 environment (which is the default) to include mnctools, so it should now work as well.
$ module load payu
Loading payu/1.2.0
Loading requirement: singularity
$ python -c 'from mnctools import mnctools as mnc'
$
If this solves your issue can you mark it as the solution?
Thanks.