Yes. Rule 42 explicitly says: 'Government shall specify whether a particular department or particular activities of a department shall [be a] commercial department or undertaking.' A single department can have some activities classified as commercial (those that provide specific chargeable services) and others as service activities. Rule 44 also reflects this: 'This rule may be applied to particular units or particular activities of any department even though the department as a whole may not be a commercial department.'
Source: GAR Rule 42