Active Portal Users counts are the number of users with access to parts of the employee tools module of the portal. If you would like to change this count to more accurately portray the number of users that are using the portal, it probably means that you have given more users access than you should.
To fix these counts, go to Admin > User Access:
Any employee that has a check box next to their name in the HR section of User Access will be counted as an Active Portal User / Employee Tools User.
To reduce your counts, uncheck the check boxes next to any users that shouldn't have access to the Employee Tools module of the portal.