It depends on what is on contract.  Some contracts require contractors to perform government property management services using government systems.  When this is the  case the requirement is stated in the PWS.  So the first place to begin is inspection of the government furnished property and support section in the PWS.  There are some automated systems that contractors are not allowed to use, such as systems that support inherently governmental tasks.  The further question of "Can a contracting officer cease the contractor's use of a government property system when the contractor has been using the system in the past" is a legal question and beyond the scope of AAP.