I am afraid so.
Something you may want to check first, drain the gearbox oil and remove the PTO selector plate from the side of the PTO housing. This will enable you to see if the selector is OK, the locating stud on the selector shaft has not come out and by moving the gear into engagement with a lever or screw driver make sure it is going into gear.
If it is a two stage or "Live" clutch I still am of the opinion that it is the centre gone out of the disc. If it is NOT a "Live" clutch and the tractor still moves in all gears then it is something mechanical and removing of the PTO selector plate will allow you to get more of an idea of the cause.