Solved this on our machine by retaking the "deploy for debian" steps on https://github.com/mendix/m2ee-tools/blob/master/doc/install-1.md#deployment-tools-for-debian
wget -q -O - https://packages.mendix.com/mendix-debian-archive-key.asc | apt-key add -
apt-get update
apt-get install debian-mendix-archive-keyring
sudo apt-get install m2ee-tools