An apparatus for packaging containers of devices for pharmaceutical use includes a robotic arm movable from a gripping position, in which it picks up a container previously sealed by at least one protective sheet, to a release position in which it inserts the container into a bag through a suitable opening provided on a side of the bag; wherein the robotic arm is connected to at least one position control camera configured to read coordinates of a midpoint of the opening with respect to a lying plane on which the bag lies and/or an angle of rotation of the bag with respect to an axis perpendicular to the lying plane, so as to ensure the correct positioning and release of the container inside the bag.