Is it permissible for the inspection committee to deduct the remaining amount of the imprest from the employee's salary, even though the money is in his possession, under the pretext that he does not have a safe, despite the Director-General's awareness of this?

If acquiring a safe is the only way to protect money, then you must do so if you are able. They are not allowed to fine you as long as nothing has been lost. If they do, you are permitted to reclaim what was unjustly taken from you, provided that the method you use does not harm you and does not lead you to take more than your right.